Skip CCR Main Navigation National Cancer Institute National Cancer Institute U.S. National Institutes of Health www.cancer.gov
CCR - For Our Staff| Home |

Our Science – Nussinov Website

Ruth Nussinov, Ph.D.

Selected Publications

1)  Nussinov R, Tsai CJ, Mattos C.
"Pathway drug cocktail": targeting Ras signaling based on structural pathways.
Trends Mol Med. 19: 695-704, 2013.
[Journal]
2)  Tsai CJ, Nussinov R.
The molecular basis of targeting protein kinases in cancer therapeutics.
Semin. Cancer Biol. 23: 235-42, 2013.
[Journal]
3)  Nussinov R, Tsai CJ.
Allostery in disease and in drug discovery.
Cell. 153: 293-305, 2013.
[Journal]
4)  Nussinov R, Tsai CJ, Ma B.
The underappreciated role of allostery in the cellular network.
Annu Rev Biophys. 42: 169-89, 2013.
[Journal]
5)  Nussinov R.
The spatial structure of cell signaling systems.
Phys Biol. 10: 045004, 2013.
[Journal]
6)  Huang Q, Yu L, Levine AJ, Nussinov R, Ma B.
Dipeptide analysis of p53 mutations and evolution of p53 family proteins.
Biochim. Biophys. Acta. 1844: 198-206, 2014.
[Journal]
7)  Nussinov R, Ma B, Tsai C.
A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery.
Biochim. Biophys. Acta. 1834: 820-9, 2013.
[Journal]
8)  Szilagyi A, Nussinov R, Csermely P.
Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks.
Curr Top Med Chem. 13: 64-77, 2013.
[Journal]
9)  Nussinov R, Ma B, Tsai CJ, Csermely P.
Allosteric conformational barcodes direct signaling in the cell.
Structure. 21: 1509-21, 2013.
[Journal]
10)  Jang H, Connelly L, Arce FT, Ramachandran S, Lal R, Kagan BL, Nussinov R.
Alzheimer"s disease: which type of amyloid-preventing drug agents to employ?.
Phys Chem Chem Phys. 15: 8868-77, 2013.
[Journal]
11)  Qi R, Luo Y, Ma B, Nussinov R, Wei G.
Conformational Distribution and a-Helix to ß-Sheet Transition of Human Amylin Fragment Dimer.
Biomacromolecules. 2013.
[Journal]
12)  Ma B, Nussinov R.
Druggable Orthosteric and Allosteric Hot Spots to Target Protein-Protein Interactions.
Curr. Pharm. Des. 2013.
[Journal]
13)  Csermely P, Nussinov R, Szilagyi A.
Editorial (hot topic: from allosteric drugs to allo-network drugs: state of the art and trends of design, synthesis and computational methods).
Curr Top Med Chem. 13: 2-4, 2013.
[Journal]
14)  Zanuy D, Sayago FJ, Revilla-López G, Ballano G, Agemy L, Kotamraju VR, Jiménez AI, Cativiela C, Nussinov R, Sawvel AM, Stucky G, Ruoslahti E, Alemán C.
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing.
J. Comput. Aided Mol. Des. 27: 31-43, 2013.
[Journal]
15)  Kuzu G, Gursoy A, Nussinov R, Keskin O.
Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.
J. Proteome Res. 12: 2641-53, 2013.
[Journal]
16)  Jang H, Teran Arce F, Ramachandran S, Kagan BL, Lal R, Nussinov R.
Familial Alzheimer"s Disease Osaka Mutant (?E22) ß-Barrels Suggest an Explanation for the Different Aß1-40/42 Preferred Conformational States Observed by Experiment.
J Phys Chem B. 2013.
[Journal]
17)  Gupta K, Jang H, Harlen K, Puri A, Nussinov R, Schneider JP, Blumenthal R.
Mechanism of Membrane Permeation Induced by Synthetic ß-Hairpin Peptides.
Biophys. J. 105: 2093-103, 2013.
[Journal]
18)  Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R.
Mechanisms for the Insertion of Toxic, Fibril-like ß-Amyloid Oligomers into the Membrane.
J Chem Theory Comput. 9: 822-833, 2013.
[Journal]
19)  Luo Y, Dinkel P, Yu X, Margittai M, Zheng J, Nussinov R, Wei G, Ma B.
Molecular insights into the reversible formation of tau protein fibrils.
Chem. Commun. (Camb.). 49: 3582-4, 2013.
[Journal]
20)  Nussinov R, Ma B, Tsai CJ.
Multiple conformational selection and induced fit events take place in allosteric propagation.
Biophys. Chem. 2013.
[Journal]
21)  Engin HB, Gursoy A, Nussinov R, Keskin O.
Network-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View.
Curr. Pharm. Des. 2013.
[Journal]
22)  Lengauer T, Nussinov R.
New Methods Section in PLOS Computational Biology.
PLoS Comput. Biol. 9: e1002972, 2013.
[Journal]
23)  Xu Y, Wang H, Nussinov R, Ma B.
Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome.
Proteomics. 13: 1339-51, 2013.
[Journal]
24)  Zanuy D, Kotla R, Nussinov R, Teesalu T, Sugahara KN, Alemán C, Haspel N.
Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor.
J. Struct. Biol. 182: 78-86, 2013.
[Journal]
25)  Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R.
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Pharmacol. Ther. 138: 333-408, 2013.
[Journal]
26)  Ma B, Nussinov R.
Structured Crowding and Its Effects on Enzyme Catalysis.
Top Curr Chem. [Epub ahead of print], 2013.
[Journal]
27)  Guven Maiorov E, Keskin O, Gursoy A, Nussinov R.
The structural network of inflammation and cancer: merits and challenges.
Semin. Cancer Biol. 23: 243-51, 2013.
[Journal]
28)  Nussinov R.
A Future Vision for PLOS Computational Biology.
PLOS Computational Biology. 8 (10): e1002727, 2012.
[Journal]
29)  Dickin R, Hall CJ, Taylor LK, Collings AM, Nussinov R, Bourne PE.
A Review of 2011 for PLoS Computational Biology.
PLoS Comput. Biol. 8: e1002387, 2012.
[Journal]
30)  Engin BH, Keskin O, Nussinov R, Gursoy A.
A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets.
J Chem Inf Model. 52: 2273-86, 2012.
[Journal]
31)  Capone R, Jang H, Kotler SA, Connelly L, Teran Arce F, Ramachandran S, Kagan BL, Nussinov R, Lal R.
All-d-Enantiomer of beta-Amyloid Peptide Forms Ion Channels in Lipid Bilayers.
J Chem Theory Comput. 8: 1143-1152, 2012.
[Journal]
32)  Nussinov R.
Allosteric modulators can restore function in an amino acid neurotransmitter receptor by slightly altering intra-molecular communication pathways.
Br. J. Pharmacol. 165: 2110-2, 2012.
[Journal]
33)  Nussinov R, Tsai C, Xin F, Radivojac P.
Allosteric post-translational modification codes.
Trends Biochem. Sci. 37: 447-55, 2012.
[Journal]
34)  Kagan BL, Jang H, Capone R, Teran Arce F, Ramachandran S, Lal R, Nussinov R.
Antimicrobial properties of amyloid peptides.
Mol. Pharm. 9: 708-17, 2012.
[Journal]
35)  Connelly L, Jang H, Arce FT, Capone R, Kotler SA, Ramachandran S, Kagan BL, Nussinov R, Lal R.
Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's beta-amyloid peptide: relevance to the ion channel mechanism of AD pathology.
J Phys Chem B. 116: 1728-35, 2012.
[Journal]
36)  Siddiqua A, Luo Y, Meyer V, Swanson MA, Yu X, Wei G, Zheng J, Eaton GR, Ma B, Nussinov R, Eaton SS, Margittai M.
Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau.
J. Am. Chem. Soc. 134: 10271-8, 2012.
[Journal]
37)  Korkmaz EN, Nussinov R, Haliloglu T.
Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB.
PLoS Comput. Biol. 8: e1002420, 2012.
[Journal]
38)  Haspel N, Laurent AD, Zanuy D, Nussinov R, Alemán C, Puiggalí J, Revilla-López G.
Conformational exploration of two peptides and their hybrid polymer conjugates: potentialities as self-aggregating materials.
J Phys Chem B. 116: 13941-52, 2012.
[Journal]
39)  Kuzu G, Keskin O, Gursoy A, Nussinov R.
Constructing structural networks of signaling pathways on the proteome scale.
Curr. Opin. Struct. Biol. 22: 367-77, 2012.
[Journal]
40)  Yu X, Luo Y, Dinkel P, Zheng J, Wei G, Margittai M, Nussinov R, Ma B.
Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins.
J. Biol. Chem. 287: 14950-9, 2012.
[Journal]
41)  Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Miozzo F, Veres DV, Piazza F, Nussinov R.
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review.
Curr. Protein Pept. Sci. 13: 19-33, 2012.
[Journal]
42)  Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R.
Effects of point substitutions on the structure of toxic Alzheimer's beta-amyloid channels: atomic force microscopy and molecular dynamics simulations.
Biochemistry. 51: 3031-8, 2012.
[Journal]
43)  Acuner Ozbabacan SE, Keskin O, Nussinov R, Gursoy A.
Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes.
J Struct Biol. 179: 338-46, 2012.
[Journal]
44)  Kuzu G, Keskin O, Gursoy A, Nussinov R.
Expanding the conformational selection paradigm in protein-ligand docking.
Methods Mol. Biol. 819: 59-74, 2012.
[Journal]
45)  Tuncbag N, Keskin O, Nussinov R, Gursoy A.
Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement.
Proteins. 80: 1239-49, 2012.
[Journal]
46)  Nussinov R.
How do dynamic cellular signals travel long distances?.
Mol Biosyst. 8: 22-6, 2012.
[Journal]
47)  Kar G, Keskin O, Nussinov R, Gursoy A.
Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs.
J. Proteome Res. 11: 1196-207, 2012.
[Journal]
48)  Miller Y, Ma B, Nussinov R.
Metal binding sites in amyloid oligomers: Complexes and mechanisms.
Coordination Chemistry Reviews. 254 (19-20): 2245-52, 2012.
[Journal]
49)  Zhao J, Luo Y, Jang H, Yu X, Wei G, Nussinov R, Zheng J.
Probing ion channel activity of human islet amyloid polypeptide (amylin).
Biochim. Biophys. Acta. 1818: 3121-30, 2012.
[Journal]
50)  Capone R, Jang H, Kotler SA, Kagan BL, Nussinov R, Lal R.
Probing structural features of Alzheimer's amyloid-beta pores in bilayers using site-specific amino acid substitutions.
Biochemistry. 51: 776-85, 2012.
[Journal]
51)  Nussinov R, Ma B.
Protein dynamics and conformational selection in bidirectional signal transduction.
BMC Biol. 10: 2, 2012.
[Journal]
52)  Ma B, Nussinov R.
Selective molecular recognition in amyloid growth and transmission and cross-species barriers.
J. Mol. Biol. 421: 172-84, 2012.
[Journal]
53)  Xu Y, Ma B, Nussinov R.
Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP.
J Phys Chem B. [Epub ahead of print], 2012.
[Journal]
54)  Nussinov R, Tsai CJ.
The different ways through which specificity works in orthosteric and allosteric drugs.
Curr. Pharm. Des. 18: 1311-6, 2012.
[Journal]
55)  Papp D, Lenti K, Módos D, Fazekas D, Dúl Z, Türei D, Földvári-Nagy L, Nussinov R, Csermely P, Korcsmáros T.
The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops.
FEBS Lett. 586: 1795-802, 2012.
[Journal]
56)  Liu J, Nussinov R.
The role of allostery in the ubiquitin-proteasome system.
Crit. Rev. Biochem. Mol. Biol. 48: 89-97, 2012.
[Journal]
57)  Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW.
A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method.
BMC Bioinformatics. 12: 167, 2011.
[Journal]
58)  Dickin R, Marden C, Collings AM, Nussinov R, Bourne PE.
A Review of 2010 for PLoS Computational Biology.
PLoS Comput. Biol. 7: e1002003, 2011.
[Journal]
59)  Curcó D, Zanuy D, Nussinov R, Alemán C.
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides.
J Comput Chem. 32: 607-19, 2011.
[Journal]
60)  Tsai CJ, Nussinov R.
A unified convention for biological assemblies with helical symmetry.
Acta Crystallogr. D Biol. Crystallogr. 67: 716-28, 2011.
[Journal]
61)  Nussinov R, Tsai CJ, Csermely P.
Allo-network drugs: harnessing allostery in cellular networks.
Trends Pharmacol. Sci. 32: 686-93, 2011.
[Journal]
62)  Karaca E, Tozluoglu M, Nussinov R, Haliloglu T.
Alternative Allosteric Mechanisms Can Regulate the Substrate and E2 in SUMO Conjugation.
J. Mol. Biol. 406: 620-30, 2011.
[Journal]
63)  Jang H, Arce FT, Mustata M, Ramachandran S, Capone R, Nussinov R, Lal R.
Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link.
Biophys. J. 100: 1775-83, 2011.
[Journal]
64)  Haspel N, Zanuy D, Nussinov R, Teesalu T, Ruoslahti E, Aleman C.
Binding of a C-end rule Peptide to the neuropilin-1 receptor: a molecular modeling approach.
Biochemistry. 50: 1755-62, 2011.
[Journal]
65)  Ma B, Tsai C, Haliloglu T, Nussinov R.
Dynamic allostery: linkers are not merely flexible.
Structure. 19: 907-17, 2011.
[Journal]
66)  Cohen-Gihon I, Fong JH, Sharan R, Nussinov R, Przytycka TM, Panchenko AR.
Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.
Mol Biosyst. 7: 784-92, 2011.
[Journal]
67)  Revilla-López G, Torras J, Nussinov R, Alemán C, Zanuy D.
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide.
Phys Chem Chem Phys. 13: 9986-94, 2011.
[Journal]
68)  Liu J, Nussinov R.
Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination.
J. Biol. Chem. 286: 40934-42, 2011.
[Journal]
69)  Tsai CJ, Nussinov R.
Gene-specific transcription activation via long-range allosteric shape-shifting.
Biochem. J. 439: 15-25, 2011.
[Journal]
70)  Kifer I, Nussinov R, Wolfson HJ.
GOSSIP: a method for fast and accurate global alignment of protein structures.
Bioinformatics. 27: 925-32, 2011.
[Journal]
71)  Revilla-Lopez G, Rodriguez-Ropero F, Curco D, Torras J, Isabel Calaza M, Zanuy D, Jimenez AI, Cativiela C, Nussinov R, Aleman C.
Integrating the intrinsic conformational preferences of noncoded alpha-amino acids modified at the peptide bond into the noncoded amino acids database.
Proteins. 79: 1841-52, 2011.
[Journal]
72)  Puri A, Jang H, Yavlovich A, Masood MA, Veenstra TD, Luna C, Aranda-Espinoza H, Nussinov R, Blumenthal R.
Material properties of matrix lipids determine the conformation and intermolecular reactivity of diacetylenic phosphatidylcholine in the lipid bilayer.
Langmuir. 27: 15120-8, 2011.
[Journal]
73)  Parthasarathy S, Long F, Miller Y, Xiao Y, McElheny D, Thurber K, Ma B, Nussinov R, Ishii Y.
Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's beta by solid-state NMR spectroscopy.
J. Am. Chem. Soc. 133: 3390-400, 2011.
[Journal]
74)  Yuan P, Liang K, Ma B, Zheng N, Nussinov R, Huang J.
Multiple-targeting and conformational selection in the estrogen receptor: computation and experiment.
Chem Biol Drug Des. 78: 137-49, 2011.
[Journal]
75)  Nussinov R, Panchenko AR, Przytycka T.
Physics approaches to protein interactions and gene regulation.
Phys Biol. 8: 030301, 2011.
[Journal]
76)  Ma B, Nussinov R.
Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide.
J. Biol. Chem. 286: 34244-53, 2011.
[Journal]
77)  Arce FT, Jang H, Ramachandran S, Landon PB, Nussinov R, Lal R.
Polymorphism of amyloid beta peptide in different environments: implications for membrane insertion and pore formation.
Soft Matter. 7: 5267-5273, 2011.
[Journal]
78)  Tuncbag N, Gursoy A, Nussinov R, Keskin O.
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.
Nat Protoc. 6: 1341-54, 2011.
[Journal]
79)  Cohen-Gihon I, Sharan R, Nussinov R.
Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement.
Phys Biol. 8: 035009, 2011.
[Journal]
80)  Kifer I, Nussinov R, Wolfson HJ.
Protein structure prediction using a docking-based hierarchical folding scheme.
Proteins. 79: 1759-73, 2011.
[Journal]
81)  Buch I, Tsai CJ, Wolfson HJ, Nussinov R.
Symmetry-based self-assembled nanotubes constructed using native protein structures: the key role of flexible linkers.
Protein Pept. Lett. 18: 362-72, 2011.
[Journal]
82)  Mashiach-Farkash E, Nussinov R, Wolfson HJ.
SymmRef: A flexible refinement method for symmetric multimers.
Proteins. 79: 2607-23, 2011.
[Journal]
83)  Miller Y, Ma B, Nussinov R.
Synergistic interactions between repeats in tau protein and Abeta amyloids may be responsible for accelerated aggregation via polymorphic states.
Biochemistry. 50: 5172-81, 2011.
[Journal]
84)  Pan Y, Nussinov R.
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example.
PLoS Comput. Biol. 7: e1002077, 2011.
[Journal]
85)  Miller Y, Ma B, Nussinov R.
The Unique Alzheimer's Beta-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions.
J. Am. Chem. Soc. 133: 2742-8, 2011.
[Journal]
86)  Tozluoglu M, Karaca E, Nussinov R, Haliloglu T.
A mechanistic view of the role of E3 in sumoylation.
PLoS Comput. Biol. 6(8): e1000913, 2010.
[Journal]
87)  Buch I, Fishelovitch D, London N, Raveh B, Wolfson HJ, Nussinov R.
Allosteric regulation of glycogen synthase kinase 3-Beta: a theoretical study.
Biochemistry. 49: 10890-901, 2010.
[Journal]
88)  Kar G, Keskin O, Gursoy A, Nussinov R.
Allostery and population shift in drug discovery.
Curr Opin Pharmacol. 10(6): 715-22, 2010.
[Journal]
89)  Mashiach E, Schneidman-Duhovny D, Peri A, Shavit Y, Nussinov R, Wolfson HJ.
An integrated suite of fast docking algorithms.
Proteins. 78(15): 3197-204, 2010.
[Journal]
90)  Capone R, Mustata M, Jang H, Arce FT, Nussinov R, Lal R.
Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies.
Biophysical journal. 98(11): 2644-2652, 2010.
[Journal]
91)  Yu X, Wang J, Yang J, Wang Q, Cheng SZ, Nussinov R, Zheng J.
Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties.
Biophys. J. 98(1): 27-36, 2010.
[Journal]
92)  Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R.
Beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels.
J. Mol. Biol. 404(5): 917-34, 2010.
[Journal]
93)  Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R.
CCRXP: exploring clusters of conserved residues in protein structures.
Nucleic Acids Res. 38 Suppl: W398-401, 2010.
[Journal]
94)  Zen A, Micheletti C, Keskin O, Nussinov R.
Comparing interfacial dynamics in protein-protein complexes: an elastic network approach.
BMC Struct. Biol. 10: 26, 2010.
[Journal]
95)  Ozbabacan SE, Gursoy A, Keskin O, Nussinov R.
Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery.
Curr Opin Drug Discov Devel. 13(5): 527-37, 2010.
[Journal]
96)  Revilla-Lopez G, Jimenez AI, Cativiela C, Nussinov R, Aleman C, Zanuy D.
Conformational Profile of a Proline-Arginine Hybrid.
Journal of chemical information and modeling. 50(10): 1781-1789, 2010.
[Journal]
97)  Ma B, Nussinov R.
Enzyme dynamics point to stepwise conformational selection in catalysis.
Curr Opin Chem Biol. 14(5): 652-9, 2010.
[Journal]
98)  Mashiach E, Nussinov R, Wolfson HJ.
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking.
Nucleic Acids Res. 38 Suppl: W457-61, 2010.
[Journal]
99)  Miller Y, Ma B, Tsai C, Nussinov R.
Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH.
Proc. Natl. Acad. Sci. U.S.A. 107(32): 14128-33, 2010.
[Journal]
100)  Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R.
How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?.
J Phys Chem B. 114(17): 5964-70, 2010.
[Journal]
101)  Csermely P, Palotai R, Nussinov R.
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events.
Trends Biochem. Sci. 35(10): 539-46, 2010.
[Journal]
102)  Pan Y, Nussinov R.
Lysine120 interactions with p53 response elements can allosterically direct p53 organization.
PLoS Comput. Biol. 6(8): e1000878, 2010.
[Journal]
103)  Pan Y, Tsai C, Ma B, Nussinov R.
Mechanisms of transcription factor selectivity.
Trends Genet. 26(2): 75-83, 2010.
[Journal]
104)  Liu J, Nussinov R.
Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases.
J. Mol. Biol. 396(5): 1508-23, 2010.
[Journal]
105)  Agemy L, Sugahara KN, Kotamraju VR, Gujraty K, Girard OM, Kono Y, Mattrey RF, Park J, Sailor MJ, Jimenez AI, Cativiela C, Zanuy D, Sayago FJ, Aleman C, Nussinov R, Ruoslahti E.
Nanoparticle-induced vascular blockade in human prostate cancer.
Blood. 116(15): 2847-56, 2010.
[Journal]
106)  Revilla-Lopez G, Torras J, Curco D, Casanovas J, Calaza MI, Zanuy D, Jimanez AI, Cativiela C, Nussinov R, Grodzinski P, Aleman C.
NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids.
J Phys Chem B. 114(21): 7413-22, 2010.
[Journal]
107)  Ma B, Nussinov R.
Polymorphic C-terminal {beta}-Sheet Interactions Determine the Formation of Fibril or Amyloid {beta}-derived Diffusible Ligand-like Globulomer for the Alzheimer A{beta}42 Dodecamer.
J. Biol. Chem. 285: 37102-10, 2010.
[Journal]
108)  Miller Y, Ma B, Nussinov R.
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape.
Chem. Rev. 110(8): 4820-38, 2010.
[Journal]
109)  Pan Y, Nussinov R.
Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios.
J. Mol. Recognit. 23: 232-40, 2010.
[Journal]
110)  Liu J, Nussinov R.
Rbx1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation.
Biophys. J. 99(3): 736-44, 2010.
[Journal]
111)  Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R.
Structural convergence among diverse, toxic beta-sheet ion channels.
J Phys Chem B. 114(29): 9445-51, 2010.
[Journal]
112)  Jang H, Arce FT, Ramachandran S, Capone R, Azimova R, Kagan BL, Nussinov R, Lal R.
Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome.
Proc. Natl. Acad. Sci. U.S.A. 107(14): 6538-43, 2010.
[Journal]
113)  Ma B, Tsai C, Pan Y, Nussinov R.
Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?.
ACS Chem. Biol. 5(3): 265-72, 2010.
[Journal]
114)  Miller Y, Ma B, Nussinov R.
Zinc ions promote Alzheimer A{beta} aggregation via population shift of polymorphic states.
Proc. Natl. Acad. Sci. U.S.A. 107(21): 9490-5, 2010.
[Journal]
115)  Tuncbag N, Kar G, Keskin O, Gursoy A, Nussinov R.
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.
Brief. Bioinformatics. 10(3): 217-32, 2009.
[Journal]
116)  Ma B, Nussinov R.
Amplification of signaling via cellular allosteric relay and protein disorder.
Proc. Natl. Acad. Sci. U.S.A. 106 (17): 6887-8, 2009.
[Journal]
117)  Buch I, Brooks BR, Wolfson HJ, Nussinov R.
Computational validation of protein nanotubes.
Nano Lett. 9: 1096-102, 2009.
[Journal]
118)  Alemán C, Jiménez AI, Cativiela C, Nussinov R, Casanovas J.
Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue.
J. Org. Chem. 74: 7834-43, 2009.
[Journal]
119)  Pan Y, Nussinov R.
Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view.
PLoS Comput. Biol. 5(7): e1000448, 2009.
[Journal]
120)  Carbonell P, Nussinov R, del Sol A.
Energetic determinants of protein binding specificity: insights into protein interaction networks.
Proteomics. 9: 1744-53, 2009.
[Journal]
121)  Mashiach E, Nussinov R, Wolfson HJ.
FiberDock: Flexible induced-fit backbone refinement in molecular docking.
Proteins. 78: 1503-1519, 2009.
[Journal]
122)  Pan Y, Tsai C, Ma B, Nussinov R.
How do transcription factors select specific binding sites in the genome?.
Nat. Struct. Mol. Biol. 16(11): 1118-20, 2009.
[Journal]
123)  Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C.
In silico molecular engineering for a targeted replacement in a tumor-homing peptide.
J Phys Chem B. 113: 7879-89, 2009.
[Journal]
124)  Zanuy D, Curcó D, Nussinov R, Alemán C.
Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide.
Biopolymers. 92: 83-93, 2009.
[Journal]
125)  Tsai CJ, Ma B, Nussinov R.
Intra-molecular chaperone: the role of the N-terminal in conformational selection and kinetic control.
Physical biology. 6: 13001, 2009.
[Journal]
126)  Mustata M, Capone R, Jang H, Arce FT, Ramachandran S, Lal R, Nussinov R.
K3 Fragment of Amyloidogenic beta(2)-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis.
J. Am. Chem. Soc. 131(41): 14938-45, 2009.
[Journal]
127)  Jang H, Arce FT, Capone R, Ramachandran S, Lal R, Nussinov R.
Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels.
Biophys. J. 97(11): 3029-37, 2009.
[Journal]
128)  Yu X, Wang Q, Yang JC, Buch I, Tsai CJ, Ma B, Cheng SZ, Nussinov R, Zheng J.
Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain.
Biomacromolecules. 10: 390-9, 2009.
[Journal]
129)  Dror O, Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.
Novel approach for efficient pharmacophore-based virtual screening: method and applications.
Journal of chemical information and modeling. 49(10): 2333-43, 2009.
[Journal]
130)  Miller Y, Ma B, Nussinov R.
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation.
Biophys. J. 97(4): 1168-77, 2009.
[Journal]
131)  Tsai CJ, Del Sol A, Nussinov R.
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms.
Mol Biosyst. 5: 207-16, 2009.
[Journal]
132)  Pappu RV, Nussinov R.
Protein folding: lessons learned and new frontiers. Preface.
Physical biology. 6: 10301, 2009.
[Journal]
133)  Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C.
Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale.
Journal of chemical information and modeling. 49: 1623-9, 2009.
[Journal]
134)  Tsai C, Ma B, Nussinov R.
Protein-protein interaction networks: how can a hub protein bind so many different partners?.
Trends Biochem. Sci. 34(12): 594-600, 2009.
[Journal]
135)  Ma B, Nussinov R.
Regulating highly dynamic unstructured proteins and their coding mRNAs.
Genome Biol. 10(1): 204, 2009.
[Journal]
136)  Shulman-Peleg A, Nussinov R, Wolfson HJ.
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases.
Nucleic Acids Res. 37: D369-73, 2009.
[Journal]
137)  Revilla-López G, Torras J, Jiménez AI, Cativiela C, Nussinov R, Alemán C.
Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue.
J. Org. Chem. 74: 2403-12, 2009.
[Journal]
138)  Liu J, Nussinov R.
The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.
PLoS Comput. Biol. 5(10): e1000527, 2009.
[Journal]
139)  del Sol A, Tsai C, Ma B, Nussinov R.
The origin of allosteric functional modulation: multiple pre-existing pathways.
Structure. 17(8): 1042-50, 2009.
[Journal]
140)  Boehr DD, Nussinov R, Wright PE.
The role of dynamic conformational ensembles in biomolecular recognition.
Nat. Chem. Biol. 5(11): 789-796, 2009.
[Journal]
141)  Fishelovitch D, Shaik S, Wolfson HJ, Nussinov R.
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism.
The journal of physical chemistry. B. 113(39): 13018-13025, 2009.
[Journal]
142)  Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R.
Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example.
Mol Biosyst. 5(12): 1770-78, 2009.
[Journal]
143)  Casanovas J, Jimenez AI, Cativiela C, Nussinov R, Aleman C.
1-Amino-2-Phenylcyclopentane-1-carboxylic Acid: A Conformationally Restricted Phenylalanine Analogue.
J Org Chem. 73: 644-51, 2008.
[Journal]
144)  Liu J, Nussinov R.
Allosteric effects in the marginally stable von Hippel Lindau tumor suppressor protein and allostery-based rescue mutant design.
Proc Natl Acad Sci U S A. 105(3): 901-6, 2008.
[Journal]
145)  Tsai C, Del Sol A, Nussinov R.
Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
J. Mol. Biol. 378(1): 1-11, 2008.
[Journal]
146)  Abraham M, Dror O, Nussinov R, Wolfson HJ.
Analysis and classification of RNA tertiary structures.
RNA. 14(11): 2274-89, 2008.
[Journal]
147)  Zheng J, Jang H, Ma B, Nussinov R.
Annular Structures as Intermediates in Fibril Formation of Alzheimer Abeta17-42.
The journal of physical chemistry. B. 112(22): 6856-65, 2008.
[Journal]
148)  Rodriguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Aleman C.
Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design.
J Chem Inf Model. 48(2): 333-43, 2008.
[Journal]
149)  Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O.
Architectures and Functional Coverage of Protein-Protein Interfaces.
J. Mol. Biol. 381(3): 785-802, 2008.
[Journal]
150)  Zheng J, Jang H, Nussinov R.
beta(2)-Microglobulin Amyloid Fragment Organization and Morphology and Its Comparison to Abeta Suggests That Amyloid Aggregation Pathways Are Sequence Specific.
Biochemistry. 47(8): 2497-509, 2008.
[Journal]
151)  Tozluoglu M, Karaca E, Haliloglu T, Nussinov R.
Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis.
Nucleic Acids Res. 36(15): 5033-49, 2008.
[Journal]
152)  Flores-Ortega A, Jimenez AI, Cativiela C, Nussinov R, Aleman C, Casanovas J.
Conformational Preferences of alpha-Substituted Proline Analogues.
J. Org. Chem. 73(9): 3418-27, 2008.
[Journal]
153)  Flores-Ortega A, Casanovas J, Nussinov R, Alemán C.
Conformational Preferences of beta- and gamma-Aminated Proline Analogues.
The journal of physical chemistry. B. 112(44): 14045-55, 2008.
[Journal]
154)  Kifer I, Nussinov R, Wolfson HJ.
Constructing templates for protein structure prediction by simulation of protein folding pathways.
Proteins. 73(2): 380-94, 2008.
[Journal]
155)  Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.
Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules.
J. Comput. Biol. 15(7): 737-54, 2008.
[Journal]
156)  Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ.
FireDock: a web server for fast interaction refinement in molecular docking.
Nucleic Acids Res. 36: W229-32, 2008.
[Journal]
157)  Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T.
HingeProt: Automated prediction of hinges in protein structures.
Proteins. 70(4): 1219-27, 2008.
[Journal]
158)  Casanovas J, Nussinov R, Aleman C.
Intrinsic Conformational Preferences of C(alpha,alpha)-Dibenzylglycine.
J. Org. Chem. 73(11): 4205-11, 2008.
[Journal]
159)  Jang H, Ma B, Lal R, Nussinov R.
Models of Toxic {beta}-sheet Channels of Protegrin-1 (PG-1) Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer {beta}-Amyloid Ion Channels.
Biophys. J. 95(10): 4631-42, 2008.
[Journal]
160)  Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R.
MolAxis: a server for identification of channels in macromolecules.
Nucleic Acids Res. 36: W210-5, 2008.
[Journal]
161)  Yaffe E, Fishelovitch D, Wolfson HJ, Halperin D, Nussinov R.
MolAxis: efficient and accurate identification of channels in macromolecules.
Proteins. 73: 72-86, 2008.
[Journal]
162)  Zheng J, Ma B, Chang Y, Nussinov R.
Molecular dynamics simulations of Alzheimer Abeta40 elongation and lateral association.
Front. Biosci. 13: 3919-30, 2008.
[Journal]
163)  Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
Nucleic Acids Res. 36: W260-4, 2008.
[Journal]
164)  Gazit E, Nussinov R.
Nanostructure design: methods and protocols. Preface.
Methods Mol. Biol. 474: v-vii, 2008.
[Journal]
165)  Jang H, Zheng J, Lal R, Nussinov R.
New structures help the modeling of toxic amyloidss ion channels.
Trends Biochem Sci. 33(2): 91-100, 2008.
[Journal]
166)  Pan Y, Nussinov R.
p53-Induced DNA Bending: The Interplay between p53-DNA and p53-p53 Interactions.
The journal of physical chemistry. B. 112(21): 6716-24, 2008.
[Journal]
167)  Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.
PharmaGist: a webserver for ligand-based pharmacophore detection.
Nucleic Acids Res. 36: W223-8, 2008.
[Journal]
168)  Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.
Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns.
J. Mol. Biol. 379(2): 299-316, 2008.
[Journal]
169)  Andrusier N, Mashiach E, Nussinov R, Wolfson HJ.
Principles of flexible protein-protein docking.
Proteins. 73(2): 271-89, 2008.
[Journal]
170)  Keskin O, Gursoy A, Ma B, Nussinov R.
Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact?.
Chem. Rev. 108(4): 1225-1244, 2008.
[Journal]
171)  Keskin O, Nussinov R, Gursoy A.
Prism: protein-protein interaction prediction by structural matching.
Methods Mol. Biol. 484: 505-21, 2008.
[Journal]
172)  Ahmad S, Keskin O, Sarai A, Nussinov R.
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.
Nucleic Acids Res. 36(18): 5922-32, 2008.
[Journal]
173)  Yogurtcu ON, Erdemli SB, Nussinov R, Turkay M, Keskin O.
Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations.
Biophys. J. 94: 3475-85, 2008.
[Journal]
174)  Buch I, Tsai CJ, Wolfson HJ, Nussinov R.
Self-assembly of fused homo-oligomers to create nanotubes.
Methods Mol. Biol. 474: 117-31, 2008.
[Journal]
175)  Ballano G, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C.
Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids.
The journal of physical chemistry. B. 112: 13101-15, 2008.
[Journal]
176)  Dror O, Schneidman-Duhovny D, Shulman-Peleg A, Nussinov R, Wolfson HJ, Sharan R.
Structural similarity of genetically interacting proteins.
BMC systems biology. 2: 69, 2008.
[Journal]
177)  Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, Nussinov R.
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima.
J. Mol. Biol. 383: 281-91, 2008.
[Journal]
178)  Zanuy D, Flores-Ortega A, Casanovas J, Curcoa D, Nussinov R, Aleman C.
The Energy Landscape of a Selective Tumor-Homing Pentapeptide.
Journal of Physical Chemistry B. 112(29): 8692-700, 2008.
[Journal]
179)  Gursoy A, Keskin O, Nussinov R.
Topological properties of protein interaction networks from a structural perspective.
Biochem. Soc. Trans. 36: 1398-1403, 2008.
[Journal]
180)  Emekli U, Gunasekaran K, Nussinov R, Haliloglu T.
What Can We Learn From Highly Connected beta-Rich Structures for Structural Interface Design?.
Methods Mol. Biol. 474: 235-53, 2008.
[Journal]
181)  Haspel N, Wainreb G, Inbar Y, Tsai HH, Tsai CJ, Wolfson HJ, Nussinov R.
A hierarchical protein folding scheme based on the building block folding model.
Methods Mol. Biol. 350: 189-204, 2007.
[Journal]
182)  Shatsky M, Nussinov R, Wolfson HJ.
Algorithms for multiple protein structure alignment and structure-derived multiple sequence alignment.
Methods Mol. Biol. 413: 125-46, 2007.
[Journal]
183)  Schneidman-Duhovny D, Nussinov R, Wolfson HJ.
Automatic prediction of protein interactions with large scale motion.
Proteins. 69(4): 764-73, 2007.
[Journal]
184)  Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R.
Changing the charge distribution of {beta}-helical based nanostructures can provide the conditions for charge transfer.
Biophys J. 93(1): 245-53, 2007.
[Journal]
185)  Curco D, Nussinov R, Aleman C.
Coarse-Grained Representation of beta-Helical Protein Building Blocks.
J Phys Chem B. 111(35): 10538-49, 2007.
[Journal]
186)  Curco D, Nussinov R, Aleman C.
Coarse-graining the Self-assembly of beta-helical Protein Building Blocks.
J Phys Chem B. 111(50): 14006-11, 2007.
[Journal]
187)  Cohen-Gihon I, Nussinov R, Sharan R.
Comprehensive analysis of co-occurring domain sets in yeast proteins.
BMC Genomics. 8: 161, 2007.
[Journal]
188)  Jang H, Ma B, Nussinov R.
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect.
BMC Struct Biol. 7: 21, 2007.
[Journal]
189)  Flores-Ortega A, Casanovas J, Zanuy D, Nussinov R, Aleman C.
Conformations of Proline Analogues Having Double Bonds in the Ring.
J Phys Chem B. 111(19): 5475-82, 2007.
[Journal]
190)  Inbar Y, Schneidman-Duhovny D, Dror O, Nussinov R, Wolfson H.
Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules (11th Annual International Conference, RECOMB 2007).
Volume LNBI 4453. p. 412-29. [Meeting Proceeding]
191)  Dror O, Lasker K, Nussinov R, Wolfson H.
EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies.
Acta Crystallogr. D Biol. Crystallogr. 63: 42-9, 2007.
[Journal]
192)  Lasker K, Dror O, Shatsky M, Nussinov R, Wolfson HJ.
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 4: 28-39, 2007.
[Journal]
193)  Andrusier N, Nussinov R, Wolfson HJ.
FireDock: Fast interaction refinement in molecular docking.
Proteins. 69(1): 139-59, 2007.
[Journal]
194)  Gunasekaran K, Nussinov R.
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding.
J. Mol. Biol. 365: 257-73, 2007.
[Journal]
195)  Casanovas J, Zanuy D, Nussinov R, Alemán C.
Intrinsic conformational characteristics of alpha,alpha-diphenylglycine.
J. Org. Chem. 72: 2174-81, 2007.
[Journal]
196)  Hu Z, Bowen D, Southerland WM, Del Sol A, Pan Y, Nussinov R, Ma B.
Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR.
PLoS Comput Biol. 3: e117, 2007.
[Journal]
197)  Zheng J, Jang H, Ma B, Tsai C, Nussinov R.
Modeling the Alzheimer A{beta}17-42 Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities.
Biophys J. 93(9): 3046-57, 2007.
[Journal]
198)  Jang H, Zheng J, Nussinov R.
Models of {beta}-Amyloid Ion-Channels in the Membrane Suggest that Channel Formation in the Bilayer is a Dynamic Process.
Biophys J. 93(6): 1938-49, 2007.
[Journal]
199)  Del Sol A, Arauzo-Bravo MJ, Amoros Moya D, Nussinov R.
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.
Genome Biol. 8(5): R92, 2007.
[Journal]
200)  Zheng J, Zanuy D, Haspel N, Tsai CJ, Aleman C, Nussinov R.
Nanostructure Design Using Protein Building Blocks Enhanced by Conformationally Constrained Synthetic Residues.
Biochemistry. 46: 1205-1218, 2007.
[Journal]
201)  Tsai C, Zheng J, Zanuy D, Haspel N, Wolfson H, Alemán C, Nussinov R.
Principles of nanostructure design with protein building blocks.
Proteins. 68(1): 1-12, 2007.
[Journal]
202)  Fishelovitch D, Hazan C, Hirao H, Wolfson HJ, Nussinov R, Shaik S.
QM/MM Study of the Active Species of the Human Cytochrome P450 3A4, and the Influence Thereof of the Multiple Substrate Binding.
J Phys Chem B. 111(49): 13822-32, 2007.
[Journal]
203)  Ma B, Pan Y, Zheng J, Levine AJ, Nussinov R.
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.
Nucleic Acids Res. 35(9): 2986-3001, 2007.
[Journal]
204)  Keskin O, Nussinov R.
Similar binding sites and different partners: implications to shared proteins in cellular pathways.
Structure. 15: 341-54, 2007.
[Journal]
205)  Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.
Spatial chemical conservation of hot spot interactions in protein-protein complexes.
BMC Biol. 5: 43, 2007.
[Journal]
206)  Zanuy D, Rodríguez-Ropero F, Haspel N, Zheng J, Nussinov R, Aleman C.
Stability of Tubular Structures Based on beta-Helical Proteins: Self-Assembled versus Polymerized Nanoconstructs and Wild-Type versus Mutated Sequences.
Biomacromolecules. 8(10): 3135-46, 2007.
[Journal]
207)  Pan Y, Nussinov R.
Structural basis for p53 binding-induced DNA bending.
J. Biol. Chem. 282: 691-9, 2007.
[Journal]
208)  Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R.
Structural Dynamics of the Cooperative Binding of Organic Molecules in the Human Cytochrome P450 3A4.
J Am Chem Soc. 129: 1602-1611, 2007.
[Journal]
209)  Zanuy D, Rodríguez-Ropero F, Nussinov R, Alemán C.
Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study.
J Struct Biol. 160(2): 177-89, 2007.
[Journal]
210)  Keskin O, Gursoy A, Ma B, Nussinov R.
Towards drugs targeting multiple proteins in a systems biology approach.
Current topics in medicinal chemistry. 7: 945-53, 2007.
[Journal]
211)  Ma B, Nussinov R.
Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design.
Current topics in medicinal chemistry. 7: 1007-13, 2007.
[Journal]
212)  Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C.
Use of constrained synthetic amino acids in beta-helix proteins for conformational control.
The journal of physical chemistry. B. 111: 3236-42, 2007.
[Journal]
213)  Dror O, Shulman-Peleg A, Nussinov R, Wolfson H.
Predicting Molecular Interactions In Silico: I. An Updated Guide to Pharmacophore Identification and its Applications to Drug Design. In: Frontiers in Medicinal Chemistry. Volume 3.
Ewing Township: Bethan Science Publishers; 2006. p. 551-584 [Book Chapter]
214)  Liu J, Pan Y, Ma B, Nussinov R.
'Similarity Trap' in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains.
Structure. 14: 1811-21, 2006.
[Journal]
215)  Wainreb G, Haspel N, Wolfson HJ, Nussinov R.
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly.
Bioinformatics. 22(11): 1343-1352, 2006.
[Journal]
216)  Ertekin A, Nussinov R, Haliloglu T.
Association of putative concave protein-binding sites with the fluctuation behavior of residues.
Protein Sci. 15: 2265-77, 2006.
[Journal]
217)  Gnanakaran S, Nussinov R, García AE.
Atomic-level description of amyloid beta-dimer formation.
J. Am. Chem. Soc. 128: 2158-9, 2006.
[Journal]
218)  Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R.
Backbone Conformational Preferences and Pseudorotational Ring Puckering of 1-Aminocyclopentane-1-carboxylic Acid.
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 110: 21264-21271, 2006.
[Journal]
219)  Pan Y, Ma B, Levine AJ, Nussinov R.
Comparison of the Human and Worm p53 Structures Suggests a Way for Enhancing Stability.
Biochemistry. 45: 3925-3933, 2006.
[Journal]
220)  Zanuy D, Gunasekaran K, Lesk AM, Nussinov R.
Computational Study of the Fibril Organization of Polyglutamine Repeats Reveals a Common Motif Identified in beta-Helices.
J Mol Biol. 358(1): 330-45, 2006.
[Journal]
221)  Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R.
Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids.
Phys Biol. 3: S54-62, 2006.
[Journal]
222)  Zheng J, Ma B, Nussinov R.
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure.
Physical biology. 3: P1-4, 2006.
[Journal]
223)  Halperin I, Wolfson H, Nussinov R.
Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
Proteins. 63(4): 832-45, 2006.
[Journal]
224)  Haspel N, Zanuy D, Alemán C, Wolfson H, Nussinov R.
De Novo Tubular Nanostructure Design Based on Self-Assembly of beta-Helical Protein Motifs.
Structure. 14: 1137-48, 2006.
[Journal]
225)  Tsai CJ, Zheng J, Nussinov R.
Designing a nanotube using naturally occurring protein building blocks.
PLoS Comput Biol. 2: e42, 2006.
[Journal]
226)  Zanuy D, Nussinov R, Alemán C.
From peptide-based material science to protein fibrils: discipline convergence in nanobiology.
Phys Biol. 3: S80-90, 2006.
[Journal]
227)  Casanovas J, Zanuy D, Nussinov R, Aleman C.
Identification of the intrinsic conformational properties of 1-aminocyclobutane-1-carboxylic acid.
Chemical Physics Letters. 429: 558-62, 2006.
[Journal]
228)  Jang H, Ma B, Woolf TB, Nussinov R.
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect.
Biophys. J. 91: 2848-59, 2006.
[Journal]
229)  Nussinov R, Aleman C.
Nanobiology: from physics and engineering to biology.
Physical Biology. 3: 1, 2006.
[Journal]
230)  Shatsky M, Nussinov R, Wolfson HJ.
Optimization of multiple-sequence alignment based on multiple-structure alignment.
Proteins. 62: 209-17, 2006.
[Journal]
231)  Shaul S, Nussinov R, Pupko T.
Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms.
BMC Evol Biol. 6: 22, 2006.
[Journal]
232)  del Sol A, Fujihashi H, Amoros D, Nussinov R.
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families.
Protein Sci. 15: 2120-8, 2006.
[Journal]
233)  del Sol A, Fujihashi H, Amoros D, Nussinov R.
Residues crucial for maintaining short paths in network communication mediate signaling in proteins.
Mol. Syst. Biol. 2: 2006.0019, 2006.
[Journal]
234)  Tsai HH, Gunasekaran K, Nussinov R.
Sequence and structure analysis of parallel Beta helices: implication for constructing amyloid structural models.
Structure. 14: 1059-72, 2006.
[Journal]
235)  Ma B, Nussinov R.
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation.
Current opinion in chemical biology. 10: 445-52, 2006.
[Journal]
236)  Zheng J, Ma B, Tsai C, Nussinov R.
Structural Stability and Dynamics of an Amyloid-forming Peptide GNNQQNY from the Yeast Prion Sup-35.
Biophys J. 91(3): 824-33, 2006.
[Journal]
237)  Tsai CJ, Zheng J, Alemán C, Nussinov R.
Structure by design: from single proteins and their building blocks to nanostructures.
Trends Biotechnol. 24: 449-54, 2006.
[Journal]
238)  Dror O, Nussinov R, Wolfson HJ.
The ARTS web server for aligning RNA tertiary structures.
Nucleic Acids Res. 34: W412-5, 2006.
[Journal]
239)  Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson HJ.
The multiple common point set problem and its application to molecule binding pattern detection.
J Comput Biol. 13: 407-28, 2006.
[Journal]
240)  Ma B, Nussinov R.
The Stability of Monomeric Intermediates Controls Amyloid Formation: A{beta}25-35 and its N27Q Mutant.
Biophys J. 90(10): 3365-3374, 2006.
[Journal]
241)  Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R.
Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface.
Proc Natl Acad Sci U S A. 102: 3988-93, 2005.
[Journal]
242)  Keskin O, Nussinov R.
Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways.
Protein Eng Des Sel. 18: 11-24, 2005.
[Journal]
243)  Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Dror O, Shulman-Peleg A, Ma B, Nussinov R.
From structure to function: methods and applications.
Curr Protein Pept Sci. 6: 171-83, 2005.
[Journal]
244)  Inbar Y, Benyamini H, Nussinov R, Wolfson HJ.
Prediction of multimolecular assemblies by multiple docking.
J Mol Biol. 349: 435-47, 2005.
[Journal]
245)  Tsai CJ, Nussinov R.
Protein-protein interactions. Principles and prediction.
Phys. Biol. 2: 51, 2005.
[Journal]
246)  Haspel N, Zanuy D, Tsai HH(G), Ma B, Wolfson H, Nussinov R.
Sipe JD, eds.
Computational approaches and tools for establishing structural models for. In: Amyloid Proteins. Volume 1.
Weinheim: Wiley VCH Lerlag; 2005. p. 301-18 [Book Chapter]
247)  Benyamini H, Gunasekaran K, Wolfson H, Nussinov R.
Sipe JD, eds.
Gelsolin. In: Amyloid Proteins. Volume 1.
Weinheim: Wiley-VCH Verlag; 2005. p. 625-34 [Book Chapter]
248)  Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R.
A Comparative Study of Amyloid Fibril Formation by Residues 15-19 of the Human Calcitonin Hormone: A Single beta-Sheet Model with a Small Hydrophobic Core.
J Mol Biol. 345: 1213-27, 2005.
[Journal]
249)  Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ.
Approaching the CAPRI challenge with an efficient geometry-based docking.
Proteins. 60: 217-23, 2005.
[Journal]
250)  Dror O, Nussinov R, Wolfson H.
ARTS: alignment of RNA tertiary structures.
Bioinformatics. 21 Suppl 2: ii47-ii53, 2005.
[Journal]
251)  Pan Y, Ma B, Nussinov R.
CD4 Binding Partially Locks the Bridging Sheet in gp120 but Leaves the beta2/3 Strands Flexible.
J Mol Biol. 350: 514-27, 2005.
[Journal]
252)  Inbar Y, Benyamini H, Nussinov R, Wolfson HJ.
Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies.
Phys Biol. 2: S156-65, 2005.
[Journal]
253)  Lasker K, Dror O, Benyamini H, Nussinov R, Wolfson HJ.
Discovery of Protein Substructures in EM Maps.
Lecture Notes in Computer Science. 3692: 423-34, 2005.
[Journal]
254)  Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R.
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.
Proc Natl Acad Sci U S A. 102: 8174-9, 2005.
[Journal]
255)  Benyamini H, Gunasekaran K, Wolfson H, Nussinov R.
Fibril modelling by sequence and structure conservation analysis combined with protein docking techniques: beta(2)-microglobulin amyloidosis.
Biochim Biophys Acta. 1753(1): 121-30, 2005.
[Journal]
256)  Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R.
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions.
Proteins. 61: 6-20, 2005.
[Journal]
257)  Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.
Geometry-based flexible and symmetric protein docking.
Proteins. 60: 224-31, 2005.
[Journal]
258)  Keskin O, Ma B, Nussinov R.
Hot Regions in Protein-Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues.
J Mol Biol. 345: 1281-1294, 2005.
[Journal]
259)  Haliloglu T, Keskin O, Ma B, Nussinov R.
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
Biophys J. 88: 1552-9, 2005.
[Journal]
260)  Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R.
In the Quest for Stable Rescuing Mutants of p53: Computational Mutagenesis of Flexible Loop L1.
Biochemistry. 44: 1423-1432, 2005.
[Journal]
261)  Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ.
MAPPIS: Multiple 3D Alignment of Protein-Protein Interfaces.
Lecture Notes in Computer Science. 3695: 91-103, 2005.
[Journal]
262)  Inbar Y, Wolfson HJ, Nussinov R.
Multiple Docking for Protein Structure Prediction.
International Journal of Robotics Research. 24: 109-30, 2005.
[Journal]
263)  Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.
PatchDock and SymmDock: servers for rigid and symmetric docking.
Nucleic Acids Res. 33: W363-7, 2005.
[Journal]
264)  Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A.
PRISM: protein interactions by structural matching.
Nucleic Acids Res. 33: W331-6, 2005.
[Journal]
265)  Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A.
PRISM: protein interactions by structural matching.
Nucleic Acids Res. 33: W331-6, 2005.
[Journal]
266)  Keskin O, Ma B, Rogale K, Gunasekaran K, Nussinov R.
Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach.
Phys Biol. 2: S24-S35, 2005.
[Journal]
267)  Shulman-Peleg A, Mintz S, Nussinov R, Wolfson HJ.
Protein-protein interfaces: recognition of similar spatial and chemical organizations.
Lecture Notes in computer Science. 3240: 194-205, 2005.
[Journal]
268)  Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson HJ.
Recognition of binding patterns common to a set of protein structure.
Lecture Notes in Computer Science. 3500: 440-55, 2005.
[Journal]
269)  Shulman-Peleg A, Nussinov R, Wolfson HJ.
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces.
Nucleic Acids Res. 33: W337-41, 2005.
[Journal]
270)  Ma B, Pan Y, Gunasekaran K, Keskin O, Venkataraghavan RB, Levine AJ, Nussinov R.
The contribution of the Trp/Met/Phe residues to physical interactions of p53 with cellular proteins.
Phys Biol. 2: S56-66, 2005.
[Journal]
271)  Tsai CJ, Nussinov R.
The implications of higher (or lower) success in secondary structure prediction of chain fragments.
Protein Sci. 14: 1943-4, 2005.
[Journal]
272)  Shatsky M, Nussinov R, Wolfson HJ.
A method for simultaneous alignment of multiple protein structures.
Proteins. 56: 143-56, 2004.
[Journal]
273)  Keskin O, Tsai CJ, Wolfson H, Nussinov R.
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
Protein Sci. 13: 1043-55, 2004.
[Journal]
274)  Gunasekaran K, Tsai CJ, Nussinov R.
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.
J Mol Biol. 341: 1327-41, 2004.
[Journal]
275)  Shatsky M, Dror O, Schneidman-Duhovny D, Nussinov R, Wolfson HJ.
BioInfo3D: a suite of tools for structural bioinformatics.
Nucleic Acids Res. 32: W503-7, 2004.
[Journal]
276)  Pan Y, Ma B, Keskin O, Nussinov R.
Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain.
J Biol Chem. 279: 30523-30, 2004.
[Journal]
277)  Kumar S, Nussinov R.
Different roles of electrostatics in heat and in cold: adaptation by citrate synthase.
Chembiochem. 5: 280-90, 2004.
[Journal]
278)  Kumar S, Nussinov R.
Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability.
Biophys Chem. 111: 235-46, 2004.
[Journal]
279)  Shatsky M, Nussinov R, Wolfson HJ.
FlexProt: alignment of flexible protein structures without a predefinition of hinge regions.
J Comput Biol. 11: 83-106, 2004.
[Journal]
280)  Ma B, Nussinov R.
From computational quantum chemistry to computational biology: experiments and computations are (full) partners.
Phys Biol. 1: P23-6, 2004.
[Journal]
281)  Tsai HH, Tsai CJ, Ma B, Nussinov R.
In silico protein design by combinatorial assembly of protein building blocks.
Protein Sci. 13: 2753-65, 2004.
[Journal]
282)  Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R.
Insights into amyloid structural formation and assembly through computational approaches.
Amyloid. 11: 143-61, 2004.
[Journal]
283)  Gunasekaran K, Ma B, Nussinov R.
Is allostery an intrinsic property of all dynamic proteins?.
Proteins. 57: 433, 2004.
[Journal]
284)  Gunasekaran K, Nussinov R.
Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions.
Chembiochem. 5: 224-30, 2004.
[Journal]
285)  Zanuy D, Porat Y, Gazit E, Nussinov R.
Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs.
Structure (Camb). 12: 439-55, 2004.
[Journal]
286)  Barzilai A, Kumar S, Wolfson H, Nussinov R.
Potential folding-function interrelationship in proteins.
Proteins. 56: 635-49, 2004.
[Journal]
287)  Dror O, Shulman-Peleg A, Nussinov R, Wolfson HJ.
Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design.
Curr Med Chem. 11: 71-90, 2004.
[Journal]
288)  Schneidman-Duhovny D, Nussinov R, Wolfson HJ.
Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking.
Curr Med Chem. 11: 91-107, 2004.
[Journal]
289)  Li X, Keskin O, Ma B, Nussinov R, Liang J.
Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking.
J Mol Biol. 344: 781-95, 2004.
[Journal]
290)  Halperin I, Wolfson H, Nussinov R.
Protein-Protein Interactions; Coupling of Structurally Conserved Residues and of Hot Spots across Interfaces. Implications for Docking.
Structure (Camb). 12: 1027-38, 2004.
[Journal]
291)  Shulman-Peleg A, Mintz S, Nussinov R, Wolfson HJ.
Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations.
In Jonassen and J. Kim (Eds.): Algorithms in Bioinformatics: 4th Intermational Workshop, WABI, Springer Verlag. 3240: 194-205, 2004.
[Journal]
292)  Shulman-Peleg A, Nussinov R, Wolfson HJ.
Recognition of functional sites in protein structures.
J Mol Biol. 339: 607-33, 2004.
[Journal]
293)  Ma B, Nussinov R.
Release Factors eRF1 and RF2: A UNIVERSAL MECHANISM CONTROLS THE LARGE CONFORMATIONAL CHANGES.
J Biol Chem. 279: 53875-53885, 2004.
[Journal]
294)  Zanuy D, Haspel N, Tsai HH, Ma B, Gunasekaran K, Wolfson HJ, Nussinov R.
Side chain interactions determine the amyloid organization: a single layer beta-sheet molecular structure of the calcitonin peptide segment 15-19.
Phys Biol. 1: 89-99, 2004.
[Journal]
295)  Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R.
The Stability and Dynamics of the Human Calcitonin Amyloid Peptide DFNKF.
Biophys J. 87: 146-58, 2004.
[Journal]
296)  Benyamini H, Gunasekaran K, Wolfson H, Nussinov R.
Beta2-microglobulin amyloidosis: insights from conservation analysis and fibril modelling by protein docking techniques.
J Mol Biol. 330: 159-74, 2003.
[Journal]
297)  Benyamini H, Gunasekaran K, Wolfson H, Nussinov R.
Conservation and amyloid formation: A study of the gelsolin-like family.
Proteins. 51: 266-82, 2003.
[Journal]
298)  Ma B, Nussinov R.
Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences.
Protein Sci. 12: 1882-1893, 2003.
[Journal]
299)  Ma B, Nussinov R.
Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences.
Protein Sci. 12: 1882-93, 2003.
[Journal]
300)  Gunasekaran K, Tsai CJ, Kumar S, Zanuy D, Nussinov R.
Extended disordered proteins: targeting function with less scaffold.
Trends Biochem Sci. 28: 81-5, 2003.
[Journal]
301)  Haspel N, Tsai CJ, Wolfson H, Nussinov R.
Hierarchical protein folding pathways: a computational study of protein fragments.
Proteins. 51: 203-15, 2003.
[Journal]
302)  Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R.
Interdependence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I.
Biochemistry. 42: 3674-87, 2003.
[Journal]
303)  Dror O, Benyamini H, Nussinov R, Wolfson H.
MASS: multiple structural alignment by secondary structures.
Bioinformatics. 19 Suppl 1: I95-I104, 2003.
[Journal]
304)  Ma B, Nussinov R.
Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.
Protein Eng. 16: 561-75, 2003.
[Journal]
305)  Dror O, Benyamini H, Nussinov R, Wolfson HJ.
Multiple structural alignment by secondary structures: algorithm and applications.
Protein Sci. 12: 2492-507, 2003.
[Journal]
306)  Dror O, Benyamini H, Nussinov R, Wolfson HJ.
Multiple structural alignment by secondary structures: algorithm and applications.
Protein Sci. 12: 2492-507, 2003.
[Journal]
307)  Inbar Y, Benyamini H, Nussinov R, Wolfson HJ.
Protein structure prediction via combinatorial assembly of sub-structural units.
Bioinformatics. 19 Suppl 1: I158-I168, 2003.
[Journal]
308)  Ma B, Elkayam T, Wolfson H, Nussinov R.
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces.
Proc Natl Acad Sci U S A. 100(10): 5772-7, 2003.
[Journal]
309)  Haspel N, Tsai CJ, Wolfson H, Nussinov R.
Reducing the computational complexity of protein folding via fragment folding and assembly.
Protein Sci. 12: 1177-87, 2003.
[Journal]
310)  Zanuy D, Ma B, Nussinov R.
Short Peptide Amyloid Organization: Stabilities and Conformations of the Islet Amyloid Peptide NFGAIL.
Biophys J. 84: 1884-94, 2003.
[Journal]
311)  Halperin I, Wolfson H, Nussinov R.
SiteLight: binding-site prediction using phage display libraries.
Protein Sci. 12: 1344-59, 2003.
[Journal]
312)  Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ.
Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking.
Proteins. 52: 107-12, 2003.
[Journal]
313)  Kumar S, Tsai CJ, Nussinov R.
Temperature range of thermodynamic stability for the native state of reversible two-state proteins.
Biochemistry. 42: 4864-73, 2003.
[Journal]
314)  Zanuy D, Nussinov R.
The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.
J Mol Biol. 329: 565-84, 2003.
[Journal]
315)  Gunasekaran K, Ma B, Nussinov R.
Triggering loops and enzyme function: identification of loops that trigger and modulate movements.
J Mol Biol. 332: 143-59, 2003.
[Journal]
316)  Oron A, Wolfson H, Gunasekaran K, Nussinov R.
Using DelPhi to compute electrostatic potentials and assess their contribution to interactions.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 8: Unit 8.4, 2003.
[Journal]
317)  Nussinov R, Ma B, Wolfson H.
Jiang T, Smith T, Xu Y, Zhang MQ, eds.
Computational methods for docking and for drug design: Functional epitopes and combinatorial libraries. In: Current Topics in Computational Biology.
Boston: MIT Press; 2002. p. 503-24 [Book Chapter]
318)  Haspel N, Tsai CJ, Wolfson H, Nussinov R.
Tsigelny I, eds.
From the building blocks folding model to protein structure prediction. In: Protein Structure Prediction: Bioinformatic Approach.
LaJolla: International Univerity Line; 2002. p. 201-26 [Book Chapter]
319)  Kumar S, Barzilai A, Haspel N, Sham YY, Tsai CJ, Wolfson HJ, Nussinov R.
Gromiha MH, Selvarage S, eds.
Critical building blocks in proteins: A common theme in folding and binding. In: Recent Research Devleopments in Protein Folding, Stability and Design.
Trivandrum: Research Signpost; 2002. p. 207-17 [Book Chapter]
320)  Kumar S, Nussinov R.
Close-range electrostatic interactions in proteins.
Chembiochem. 3: 604-17, 2002.
[Journal]
321)  Tsai CJ, Polverino de Laureto P, Fontana A, Nussinov R.
Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins.
Protein Sci. 11: 1753-70, 2002.
[Journal]
322)  Sandak B, Nussinov R, Wolfson HJ.
Efficient unbound docking of rigid molecules.
Proceedings of ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. 2452: 185-200, 2002.
[Journal]
323)  Shatsky M, Nussinov R, Wolfson HJ.
Flexible protein alignment and hinge detection.
Proteins. 48: 242-56, 2002.
[Journal]
324)  Kumar S, Tsai CJ, Nussinov R.
Maximal stabilities of reversible two-state proteins.
Biochemistry. 41: 5359-74, 2002.
[Journal]
325)  Ma B, Nussinov R.
Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation.
Protein Sci. 11: 2335-50, 2002.
[Journal]
326)  Ma B, Shatsky M, Wolfson HJ, Nussinov R.
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations.
Protein Sci. 11: 184-97, 2002.
[Journal]
327)  Shatsky M, Nussinov R, Wolfson H.
MultiProt: A multiple protein structural alighment.
Proceedings of ALGO 02. Algorithms in Bioinformatics. Lecture Notes in Computer Science. 2452: 235-250, 2002.
[Journal]
328)  Halperin I, Ma B, Wolfson H, Nussinov R.
Principles of docking: An overview of search algorithms and a guide to scoring functions.
Proteins. 47: 409-43, 2002.
[Journal]
329)  Kumar S, Nussinov R.
Relationship between ion pair geometries and electrostatic strengths in proteins.
Biophys J. 83: 1595-612, 2002.
[Journal]
330)  Ma B, Nussinov R.
Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects.
Proc Natl Acad Sci U S A. 99: 14126-31, 2002.
[Journal]
331)  Tsai CJ, Maizel JV, Nussinov R.
The hydrophobic effect: a new insight from cold denaturation and a two-state water structure.
Crit Rev Biochem Mol Biol. 37: 55-69, 2002.
[Journal]
332)  Sham YY, Ma B, Tsai CJ, Nussinov R.
Thermal unfolding molecular dynamics simulation of Escherichia coli dihydrofolate reductase: thermal stability of protein domains and unfolding pathway.
Proteins. 46: 308-20, 2002.
[Journal]
333)  Tsai CJ, Ma B, Kumar S, Sham Y, Wolfson H, Nussionv R.
A hierarchical, building-blocks based computational scheme for protein structure prediction.
IBM Journal of Research and Development. 45: 513-23, 2001.
[Journal]
334)  Sinha N, Tsai CJ, Nussinov R.
A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer.
Protein Eng. 14: 93-103, 2001.
[Journal]
335)  Leibowitz N, Fligelman ZY, Nussinov R, Wolfson HJ.
Automated multiple structure alignment and detection of a common substructural motif.
Proteins. 43: 235-45, 2001.
[Journal]
336)  Sinha N, Tsa CJ, Nussinov R.
Building blocks, hinge-bending motions and protein topology.
J Biomol Struct Dyn. 19: 369-80, 2001.
[Journal]
337)  Kumar S, Nussinov R.
Fluctuations in ion pairs and their stabilities in proteins.
Proteins. 43: 433-54, 2001.
[Journal]
338)  Kumar S, Nussinov R.
How do thermophilic proteins deal with heat.
Cell Mol Life Sci. 58: 1216-33, 2001.
[Journal]
339)  Sinha N, Kumar S, Nussinov R.
Interdomain interactions in hinge-bending transitions.
Structure (Camb). 9: 1165-81, 2001.
[Journal]
340)  Sham YY, Ma B, Tsai CJ, Nussinov R.
Molecular dynamics simulation of Escherichia coli dihydrofolate reductase and its protein fragments: relative stabilities in experiment and simulations.
Protein Sci. 10: 135-48, 2001.
[Journal]
341)  Leibowitz N, Nussinov R, Wolfson HJ.
MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins.
J Comput Biol. 8: 93-121, 2001.
[Journal]
342)  Sinha N, Nussinov R.
Point mutations and sequence variability in proteins: redistributions of preexisting populations.
Proc Natl Acad Sci U S A. 98: 3139-44, 2001.
[Journal]
343)  Kumar S, Wolfson H, Nussionv R.
Protein flexibility and electrostatis interactions.
IBM Journal of Research and Development. 45: 499-511, 2001.
[Journal]
344)  Kumar S, Sham YY, Tsai CJ, Nussinov R.
Protein folding and function: the N-terminal fragment in adenylate kinase.
Biophys J. 80: 2439-54, 2001.
[Journal]
345)  Tsai CD, Ma B, Kumar S, Wolfson H, Nussinov R.
Protein folding: binding of conformationally fluctuating building blocks via population selection.
Crit Rev Biochem Mol Biol. 36: 399-433, 2001.
[Journal]
346)  Ma B, Wolfson HJ, Nussinov R.
Protein functional epitopes: hot spots, dynamics and combinatorial libraries.
Curr Opin Struct Biol. 11: 364-9, 2001.
[Journal]
347)  Tsai CJ, Ma B, Sham YY, Kumar S, Nussinov R.
Structured disorder and conformational selection.
Proteins. 44: 418-27, 2001.
[Journal]
348)  Tsai CJ, Nussinov R.
The building block folding model and the kinetics of protein folding.
Protein Eng. 14: 723-33, 2001.
[Journal]
349)  Kumar S, Tsai CJ, Nussinov R.
Thermodynamic differences among homologous thermophilic and mesophilic proteins.
Biochemistry. 40: 14152-65, 2001.
[Journal]
350)  Tsai CJ, Nussinov R.
Transient, highly populated, building blocks folding model.
Cell Biochem Biophys. 34: 209-35, 2001.
[Journal]
351)  Wolfson H, Nussinov R.
Webster D, eds.
Geometrical docking algorithms: A practical approach. In: Protein Structure Prediction: Methods and Protocols.
Totowa: Humana Press; 2000. p. 377-97 [Book Chapter]
352)  Ma B, Tsai CJ, Nussinov R.
A systematic study of the vibrational free energies of polypeptides in folded and random states.
Biophys J. 79: 2739-53, 2000.
[Journal]
353)  Shatsky M, Fligelman ZY, Nussinov R, Wolfson HJ.
Alignment of flexible protein structures.
Proc Int Conf Intell Syst Mol Biol. 8: 329-43, 2000.
[Journal]
354)  Tsai CJ, Maizel JV, Nussinov R.
Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape.
Proc Natl Acad Sci U S A. 97: 12038-43, 2000.
[Journal]
355)  Ma B, Tsai CJ, Nussinov R.
Binding and folding: in search of intramolecular chaperone-like building block fragments.
Protein Eng. 13: 617-27, 2000.
[Journal]
356)  Hu Z, Ma B, Wolfson H, Nussinov R.
Conservation of polar residues as hot spots at protein interfaces.
Proteins. 39: 331-42, 2000.
[Journal]
357)  Kumar S, Tsai CJ, Ma B, Nussinov R.
Contribution of salt bridges toward protein thermostability.
J. Biomol. Struct. Dyn. 1: 79-86, 2000.
[Journal]
358)  Kumar S, Ma B, Tsai CJ, Nussinov R.
Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.
Proteins. 38: 368-83, 2000.
[Journal]
359)  Kumar S, Tsai CJ, Nussinov R.
Factors enhancing protein thermostability.
Protein Eng. 13: 179-91, 2000.
[Journal]
360)  Kumar S, Nussinov R.
Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper.
Proteins. 41: 485-97, 2000.
[Journal]
361)  Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R.
Folding and binding cascades: dynamic landscapes and population shifts.
Protein Sci. 9: 10-9, 2000.
[Journal]
362)  Wolfson HJ, Nussinov R.
Geometrical docking algorithms. A practical approach.
Methods Mol Biol. 143: 377-97, 2000.
[Journal]
363)  Buyong , Xiong J, Lubkowski J, Nussinov R.
Homology modeling and molecular dynamics simulations of lymphotactin.
Protein Sci. 9: 2192-9, 2000.
[Journal]
364)  Ma B, Nussinov R.
Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces.
J Mol Biol. 296: 1091-104, 2000.
[Journal]
365)  Ma B, Kumar S, Tsai CJ, Hu Z, Nussinov R.
Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity.
J Theor Biol. 203: 383-97, 2000.
[Journal]
366)  Tsai CJ, Maizel JV, Nussinov R.
Distinguishing between sequential and nonsequentially folded proteins: implications for folding and misfolding.
Protein Sci. 8: 1591-604, 1999.
[Journal]
367)  Nussinov R, Wolfson HJ.
Efficient computational algorithms for docking and for generating and matching a library of functional epitopes I. Rigid and flexible hinge-bending docking algorithms.
Comb Chem High Throughput Screen. 2: 249-59, 1999.
[Journal]
368)  Nussinov R, Wolfson HJ.
Efficient computational algorithms for docking and for generating and matching a library of functional epitopes II. Computer vision-based techniques for the generation and utilization of functional epitopes.
Comb Chem High Throughput Screen. 2: 261-9, 1999.
[Journal]
369)  Norel R, Petrey D, Wolfson HJ, Nussinov R.
Examination of shape complementarity in docking of unbound proteins.
Proteins. 36: 307-17, 1999.
[Journal]
370)  Ma B, Nussinov R.
Explicit and implicit water simulations of a beta-hairpin peptide.
Proteins. 37: 73-87, 1999.
[Journal]
371)  Verbitsky G, Nussinov R, Wolfson H.
Flexible structural comparison allowing hinge-bending, swiveling motions.
Proteins. 34: 232-54, 1999.
[Journal]
372)  Tsai CJ, Ma B, Nussinov R.
Folding and binding cascades: shifts in energy landscapes.
Proc Natl Acad Sci U S A. 96: 9970-2, 1999.
[Journal]
373)  Ma B, Kumar S, Tsai CJ, Nussinov R.
Folding funnels and binding mechanisms.
Protein Eng. 12: 713-20, 1999.
[Journal]
374)  Kumar S, Ma B, Tsai CJ, Wolfson H, Nussinov R.
Folding funnels and conformational transitions via hinge-bending motions.
Cell Biochem Biophys. 31: 141-64, 1999.
[Journal]
375)  Tsai CJ, Kumar S, Ma B, Nussinov R.
Folding funnels, binding funnels, and protein function.
Protein Sci. 8: 1181-90, 1999.
[Journal]
376)  Leibowitz N, Fligelman ZY, Nussinov R, Wolfson HJ.
Multiple structural alignment and core detection by geometric hashing.
Proc. Int. Conf. Intell. Syst. Mol. Biol. 169-77, 1999.
[Journal]
377)  Leibowitz N, Fligelman ZY, Nussinov R, Wolfson HJ.
Multiple structural alignment and core detection by geometric hashing.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 169-77, 1999.
[Journal]
378)  Kumar S, Nussinov R.
Salt bridge stability in monomeric proteins.
J Mol Biol. 293: 1241-55, 1999.
[Journal]
379)  Norel R, Wolfson HJ, Nussinov R.
Small molecule recognition: solid angles surface representation and molecular shape complementarity.
Comb Chem High Throughput Screen. 2: 223-37, 1999.
[Journal]
380)  Wolfson H, Nussinov R.
Salzberg S, Searls D, Kasif S, eds.
.: From computer vision to protein structure association. In: .): Computational Methods in Molecular Biology.
New York: Elsevier Press; 1998. p. 313-34 [Book Chapter]
381)  Sandak B, Nussinov R, Wolfson HJ.
A method for biomolecular structural recognition and docking allowing conformational flexibility.
J Comput Biol. 5: 631-54, 1998.
[Journal]
382)  Li AJ, Nussinov R.
A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking.
Proteins. 32: 111-27, 1998.
[Journal]
383)  Lin SL, Xu D, Li A, Nussinov R.
Electrostatics, allostery, and activity of the yeast chorismate mutase.
Proteins. 31: 445-52, 1998.
[Journal]
384)  Xu D, Nussinov R.
Favorable domain size in proteins.
Fold Des. 3: 11-7, 1998.
[Journal]
385)  Sandak B, Wolfson HJ, Nussinov R.
Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers.
Proteins. 32: 159-74, 1998.
[Journal]
386)  Xu D, Tsai CJ, Nussinov R.
Mechanism and evolution of protein dimerization.
Protein Sci. 7: 533-44, 1998.
[Journal]
387)  Rosen M, Lin SL, Wolfson H, Nussinov R.
Molecular shape comparisons in searches for active sites and functional similarity.
Protein Eng. 11: 263-77, 1998.
[Journal]
388)  Norel R, Lin SL, Xu D, Wolfson H, Nussinov R.
Molecular surface variability and induced conformational changes upon protein-protein association.
Proceedings of the 10th Conversation of Stereodynamics. Structure, Motions, Interaction and Expression of Bioogical Macromolecules. 2: 33-52, 1998.
[Journal]
389)  Tsai CJ, Xu D, Nussinov R.
Protein folding via binding and vice versa.
Fold Des. 3: R71-80, 1998.
[Journal]
390)  Xu D, Tsai CJ, Nussinov R.
Hydrogen bonds and salt bridges across protein-protein interfaces.
Protein Eng. 10: 999-1012, 1997.
[Journal]
391)  Tsai CJ, Nussinov R.
Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association.
Protein Sci. 6: 1426-37, 1997.
[Journal]
392)  Tsai CJ, Nussinov R.
Hydrophobic folding units derived from dissimilar monomer structures and their interactions.
Protein Sci. 6: 24-42, 1997.
[Journal]
393)  Azarya-Sprinzak E, Naor D, Wolfson HJ, Nussinov R.
Interchanges of spatially neighbouring residues in structurally conserved environments.
Protein Eng. 10: 1109-22, 1997.
[Journal]
394)  Lin SL, Xu D, Li A, Rosen M, Wolfson HJ, Nussinov R.
Investigation of the enzymatic mechanism of the yeast chorismate mutase by docking a transition state analog.
J Mol Biol. 271: 838-45, 1997.
[Journal]
395)  Xu D, Lin SL, Nussinov R.
Protein binding versus protein folding: the role of hydrophilic bridges in protein associations.
J Mol Biol. 265: 68-84, 1997.
[Journal]
396)  Tsai CJ, Xu D, Nussinov R.
Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes.
Protein Sci. 6: 1793-805, 1997.
[Journal]
397)  Tsai CJ, Lin SL, Wolfson HJ, Nussinov R.
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect.
Protein Sci. 6: 53-64, 1997.
[Journal]
398)  Tsai CJ, Lin SL, Wolfson HJ, Nussinov R.
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique.
J Mol Biol. 260: 604-20, 1996.
[Journal]
399)  Naor D, Fischer D, Jernigan RL, Wolfson HJ, Nussinov R.
Amino acid pair interchanges at spatially conserved locations.
J Mol Biol. 256: 924-38, 1996.
[Journal]
400)  Alesker V, Nussinov R, Wolfson HJ.
Detection of non-topological motifs in protein structures.
Protein Eng. 9: 1103-19, 1996.
[Journal]
401)  Sandak B, Nussinov R, Wolfson H.
Docking of conformationally flexible molecules. Combinatrial pattern matching.
Lecture Notes in Computer Science. 1: 271-87, 1996.
[Journal]
402)  Alexandrov NN, Nussinov R, Zimmer RM.
Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
Pac Symp Biocomput. 53-72, 1996.
[Journal]
403)  Sandak B, Wolfson H, Nussinov R.
Hinge-bending at molecular interfaces: automated docking of a dihydroxyethylene - containing inhibitor to the HIV-1 protease.
Biological Structure and Dynamics (Proceedings of the 9th Conversation in Stereodynamics). Albany, Adenine Press: 233-52, 1996.
[Journal]
404)  Lin SL, Nussinov R.
Molecular recognition via face center representation of a molecular surface.
J Mol Graph. 14: 78-90, 95-7, 1996.
[Journal]
405)  Tsai CJ, Lin SL, Wolfson HJ, Nussinov R.
Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences.
Crit Rev Biochem Mol Biol. 31: 127-52, 1996.
[Journal]
406)  Tsai CJ, Lin SL, Wolfson H, Nussinov R.
Techniques for searching structural similarities between protein cores, surfaces and between protein-protein interfaces.
Techniques in Protein Chemistry. VII: 419-29, 1996.
[Journal]
407)  Fischer D, Tsai CJ, Nussinov R, Wolfson H.
A 3D sequence-independent representation of the protein data bank.
Protein Eng. 8: 981-97, 1995.
[Journal]
408)  Lin SL, Nussinov R.
A disulphide-reinforced structural scaffold shared by small proteins with diverse functions.
Nat Struct Biol. 2: 835-7, 1995.
[Journal]
409)  Fischer D, Lin SL, Wolfson HL, Nussinov R.
A geometry-based suite of molecular docking processes.
J Mol Biol. 248: 459-77, 1995.
[Journal]
410)  Lin SL, Tsai CJ, Nussinov R.
A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces.
J Mol Biol. 248: 151-61, 1995.
[Journal]
411)  Sandak B, Nussinov R, Wolfson HJ.
An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.
Comput Appl Biosci. 11: 87-99, 1995.
[Journal]
412)  Norel R, Lin SL, Wolfson HJ, Nussinov R.
Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking.
J Mol Biol. 252: 263-73, 1995.
[Journal]
413)  Sandak B, Nussinov R, Wolfson HJ.
3-D flexible docking of molecules.
Proceedings of the workshop on shape and pattern matching in combinational biology. IEEE Press: 41-54, 1994.
[Journal]
414)  Fischer D, Lin SL, Nussinov R, Wolfson H.
Docking of protein molecules.
Proceedings of the 12th International Conference on Pattern Recognition. II: Pattern recognition and neural networks: 145-49, 1994.
[Journal]
415)  Norel R, Fischer D, Wolfson HJ, Nussinov R.
Molecular surface recognition by a computer vision-based technique.
Protein Eng. 7: 39-46, 1994.
[Journal]
416)  Lin SL, Nussinov R, Fischer D, Wolfson HJ.
Molecular surface representations by sparse critical points.
Proteins. 18: 94-101, 1994.
[Journal]
417)  Norel R, Lin SL, Wolfson HJ, Nussinov R.
Shape complementarity at protein-protein interfaces.
Biopolymers. 34: 933-40, 1994.
[Journal]
418)  Fischer D, Wolfson H, Lin SL, Nussinov R.
Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
Protein Sci. 3: 769-78, 1994.
[Journal]
419)  Norel R, Fischer D, Nussinov R, Wolfson HJ.
3-D docking of protein molecules.
Proceedings of 4th Symposium on Combinatorial Pattern Matching and Lecture Notes in Computer Science. 684: 20-34, 1993.
[Journal]
420)  Bachar O, Fischer D, Nussinov R, Wolfson H.
A computer vision based technique for 3-D sequence-independent structural comparison of proteins.
Protein Eng. 6: 279-88, 1993.
[Journal]
421)  Fischer D, Wolfson H, Nussinov R.
Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications.
J Biomol Struct Dyn. 11: 367-80, 1993.
[Journal]
422)  Nussinov R.
Strong sequence patterns in eukaryotic promoter regions: potential implications for DNA structure.
Int J Biochem. 25: 597-607, 1993.
[Journal]
423)  Fischer D, Norel R, Wolfson H, Nussinov R.
Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition.
Proteins. 16: 278-92, 1993.
[Journal]
424)  Fischer D, Nussinov R, Wolfson H.
Three dimensional substructural matching in protein molecules.
Lecture Notes in Computer Science. 644: 136-50, 1993.
[Journal]
425)  Fischer D, Bachar O, Nussinov R, Wolfson H.
An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins.
J Biomol Struct Dyn. 9: 769-89, 1992.
[Journal]
426)  Nussinov R.
DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors.
J Biomol Struct Dyn. 9: 1213-37, 1992.
[Journal]
427)  Nussinov R.
DNA spatial considerations in the arrangement of G/C and A/T blocks.
Comput Biol Med. 22: 97-112, 1992.
[Journal]
428)  Nussinov R.
Intervening, looped sequences between CCAAT and TATA in proimates are rigid upstream and flexible downstream.
Proceedings of the 8th Conversation of Stereodynamics. Structure and Function: 183-212, 1992.
[Journal]
429)  Nussinov R.
The eukaryotic CCAAT and TATA boxes, DNA spacer flexibility and looping.
J Theor Biol. 155: 243-70, 1992.
[Journal]
430)  Fischer D, Nussinov R, Wolfson H.
Three dimensional substructural matching in protein molecules.
Proceedings of the 3rd Symposium on Combinatorial Pattern Matching. 133-47, 1992.
[Journal]
431)  Nussinov R.
Compositional variations in DNA sequences.
Comput Appl Biosci. 7: 287-93, 1991.
[Journal]
432)  Nussinov R.
Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences.
J Mol Evol. 33: 259-66, 1991.
[Journal]
433)  Nussinov R, Wolfson HJ.
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques.
Proc Natl Acad Sci U S A. 88: 10495-9, 1991.
[Journal]
434)  Nussinov R.
Long range and symmetry considerations in the DNA.
DNA Seq. 2: 69-79, 1991.
[Journal]
435)  Le SY, Shapiro BA, Chen JH, Nussinov R, Maizel JV.
RNA pseudoknots downstream of the frameshift sites of retroviruses.
Genet Anal Tech Appl. 8: 191-205, 1991.
[Journal]
436)  Nussinov R.
Signals in DNA sequences and their potential properties.
Comput Appl Biosci. 7: 295-9, 1991.
[Journal]
437)  Nussinov R.
The ordering of nucleotides in the DNA: strong pyrimidine-purine patterns near homooligomer tracts.
J Theor Biol. 149: 21-42, 1991.
[Journal]
438)  Nussinov R, Smythers G.
Trends in the 5' vs. 3' flanks of oligonucleotides in eukaryotic and prokaryotic genomes: the asymmetric roles played by cytosine and guanine.
J Theor Biol. 153: 111-35, 1991.
[Journal]
439)  Landau GM, Vishkin U, Nussinov R.
Fast alignment of DNA and protein sequences.
Methods Enzymol. 183: 487-502, 1990.
[Journal]
440)  Nussinov R.
General nearest neighbor preferences in G/C oligomers interrupted by A/T: correlation with DNA structure.
J Biomol Struct Dyn. 8: 399-411, 1990.
[Journal]
441)  Nussinov R.
Sequence signals in eukaryotic upstream regions.
Crit Rev Biochem Mol Biol. 25: 185-224, 1990.
[Journal]
442)  Nussinov R, Shapiro B, Le SY, Maizel JV.
Speeding up the dynamic algorithm for planar RNA folding.
Math Biosci. 100: 33-47, 1990.
[Journal]
443)  Nussionv R, Maizel Jr JV.
Studies of local stability in histone, U-snRNA and globin precursor mRNA around transcription termination sites.
Computers and Mathematics with Applications. 20: 49-56, 1990.
[Journal]
444)  Nussinov R.
Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites.
J Biomol Struct Dyn. 6: 985-1000, 1989.
[Journal]
445)  Nussinov R, Sarai A, Smythers GW, Jernigan RL.
Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA.
Biochim Biophys Acta. 1008: 329-38, 1989.
[Journal]
446)  Le SY, Owens J, Nussinov R, Chen JH, Shapiro B, Maizel JV.
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus.
Comput Appl Biosci. 5: 205-10, 1989.
[Journal]
447)  Sarai A, Mazur J, Nussinov R, Jernigan RL.
Sequence dependence of DNA conformational flexibility.
Biochemistry. 28: 7842-9, 1989.
[Journal]
448)  Nussinov R, Sarai A, Smythers GW, Wang D, Jernigan RL.
Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes.
J Biomol Struct Dyn. 7: 707-22, 1989.
[Journal]
449)  Nussinov R.
The ordering of the nucleotides in DNA: computational problems in molecular biology.
Comput Biol Med. 19: 269-81, 1989.
[Journal]
450)  Le SY, Nussinov R, Maizel JV.
Tree graphs of RNA secondary structures and their comparisons.
Comput Biomed Res. 22: 461-73, 1989.
[Journal]
451)  Owens J, Chatterjee D, Nussinov R, Konopka AK, Maizel JV.
A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features.
Comput Appl Biosci. 4: 73-7, 1988.
[Journal]
452)  Le SY, Chen JH, Nussinov R, Maizel JV.
An improved secondary structure computation method and its application to intervening sequence in the human alpha-like globin mRNA precursors.
Comput Appl Biosci. 4: 337-44, 1988.
[Journal]
453)  Nussinov R.
Conserved quartets near 5' intron junctions in primate nuclear pre-mRNA.
J Theor Biol. 133: 73-84, 1988.
[Journal]
454)  Margalit H, Shapiro BA, Nussinov R, Owens J, Jernigan RL.
Helix stability in prokaryotic promoter regions.
Biochemistry. 27: 5179-88, 1988.
[Journal]
455)  Landau GM, Vishkin U, Nussinov R.
Locating alignments with k differences for nucleotide and amino acid sequences.
Comput Appl Biosci. 4: 19-24, 1988.
[Journal]
456)  Sarai A, Mazur J, Nussinov R, Jernigan RL.
Origin of DNA helical structure and its sequence dependence.
Biochemistry. 27: 8498-502, 1988.
[Journal]
457)  Nussinov R.
Putative elements in the vicinity of viral transcription initiation sites.
Int J Biochem. 20: 721-30, 1988.
[Journal]
458)  Nussinov R, Sarai A, Wang D, Jernigan RL.
Sequence context of homooligomer tracts in eukaryotic genomes: Some DNA conformational implications.
Proceedings of the 6th Conversation of Stereodynamics. DNA Bending and Curvature: 129-38, 1988.
[Journal]
459)  Nussinov R, Sarai A, Smythers GW, Jernigan RL.
Sequence context of oligomer tracts in eukaryotic DNA: biological and conformational implications.
J Biomol Struct Dyn. 6: 543-62, 1988.
[Journal]
460)  Sarai A, Mazur J, Nussinov R, Jernigan RL.
Sequence dependence of DNA conformations: Means and fluctuations.
Proceedings of the 6th Conversation of Stereodynamics. DNA Bending and Curvature: 213-23, 1988.
[Journal]
461)  Nussinov R.
(A)GGG(A), (A)CCC(A) and other potential 3' splice signals in primate nuclear pre-mRNA sequences.
Biochim Biophys Acta. 910: 261-70, 1987.
[Journal]
462)  Landau GM, Vishkin U, Nussinov R.
An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences.
J Theor Biol. 126: 483-90, 1987.
[Journal]
463)  Shapiro BA, Nussinov R, Lipkin LE, Maizel JV.
An interactive dot matrix system for locating potentially significant features in nucleic acid molecules.
J Biomol Struct Dyn. 4: 697-706, 1987.
[Journal]
464)  Nussinov R.
Asymmetry in the distributions of the four nucleotides at mRNA initiation and 3' termini sites: some geometrical implications.
Biochim Biophys Acta. 908: 143-9, 1987.
[Journal]
465)  Nussinov R.
Conserved putative signals in 3' intron junctions in rodents.
J Biomol Struct Dyn. 4: 1051-64, 1987.
[Journal]
466)  Nussinov R.
Nucleotide quartets in the vicinity of eukaryotic transcriptional initiation sites: some DNA and chromatin structural implications.
DNA. 6: 13-22, 1987.
[Journal]
467)  Jernigan RL, Sarai A, Shapiro B, Nussinov R.
Relationship between curved DNA conformations and slow gel migration.
J Biomol Struct Dyn. 4: 561-7, 1987.
[Journal]
468)  Le SY, Currey KM, Nussinov R, Maizel JV.
Studies of frequently recurring substructures in human alpha-like globin mRNA precursors.
Comput Biomed Res. 20: 563-82, 1987.
[Journal]
469)  Nussinov R, Barber A, Maizel JV.
The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry.
J Mol Evol. 26: 187-97, 1987.
[Journal]
470)  Nussinov R.
Theoretical molecular biology: prospectives and perspectives.
J Theor Biol. 125: 219-35, 1987.
[Journal]
471)  Shapiro BA, Nussinov R, Lipkin LE, Maizel JV.
A sequence analysis system encompassing rules for DNA helical distortion.
Nucleic Acids Res. 14: 75-86, 1986.
[Journal]
472)  Landau GM, Vishkin U, Nussinov R.
An efficient string matching algorithm with k differences for nucleotide and amino acid sequences.
Nucleic Acids Res. 14: 31-46, 1986.
[Journal]
473)  Nussinov R, Weisberg RA.
Bacteriophage lambda int protein may recognize structural features of the attachment sites.
J Biomol Struct Dyn. 3: 1133-44, 1986.
[Journal]
474)  Nussinov R.
Compilation of eukaryotic sequences around transcription initiation sites.
J Theor Biol. 120: 479-87, 1986.
[Journal]
475)  Greif PC, Nussionv R, Kanehisa M, DeLisi C.
Highly nonrandom recurrence of consecutive repeats in non-coding mammalian sequences.
J. Mathematical Bioscience. 81: 43-52, 1986.
[Journal]
476)  Jernigan RL, Sarai A, Ting KL, Nussinov R.
Hydrophobic interactions in the major groove can influence DNA local structure.
J Biomol Struct Dyn. 4: 41-8, 1986.
[Journal]
477)  Nussinov R, Owens J, Maizel JV.
Sequence signals in eukaryotic upstream regions.
Biochim Biophys Acta. 866: 109-19, 1986.
[Journal]
478)  Nussinov R.
Sequence signals which may be required for efficient formation of mRNA 3' termini.
Nucleic Acids Res. 14: 3557-71, 1986.
[Journal]
479)  Nussinov R.
Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A).
Biochim Biophys Acta. 866: 93-108, 1986.
[Journal]
480)  Nussinov R.
TGTG, G clustering and other signals near non-mammalian vertebrate mRNA 3' termini: some implications.
J Biomol Struct Dyn. 3: 1145-53, 1986.
[Journal]
481)  Lennon GG, Nussinov R.
Eukaryotic oligomer frequencies are correlated with certain DNA helical parameters.
J Theor Biol. 116: 427-33, 1985.
[Journal]
482)  Nussinov R.
Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites.
J Theor Biol. 115: 179-89, 1985.
[Journal]
483)  Nussinov R.
Structural wrinkles and the genomic regulatory sites of eukaryotes.
J Mol Evol. 22: 150-9, 1985.
[Journal]
484)  Nussinov R.
The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene.
J Biomol Struct Dyn. 3: 349-61, 1985.
[Journal]
485)  Comay E, Nussinov R, Comay O.
An accelerated algorithm for calculating the secondary structure of single stranded RNAs.
Nucleic Acids Res. 12: 53-66, 1984.
[Journal]
486)  Nussinov R, Shapiro B, Lipkin LE, Maizel JV.
DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation.
J Mol Biol. 177: 591-607, 1984.
[Journal]
487)  Nussinov R.
Doublet frequencies in evolutionary distinct groups.
Nucleic Acids Res. 12: 1749-63, 1984.
[Journal]
488)  Nussinov R.
Effects of secondary structures in RNA on interlocking probabilities.
J Math Biol. 19: 95-107, 1984.
[Journal]
489)  Nussinov R, Shapiro B, Lipkin LE, Maizel JV.
Enhancer elements share local homologous twist-angle variations with a helical periodicity.
Biochim Biophys Acta. 783: 246-57, 1984.
[Journal]
490)  Nussinov R, Pieczenik G.
Folding of two large nucleotide chains.
J Theor Biol. 106: 261-73, 1984.
[Journal]
491)  Lennon GG, Nussinov R.
Homonyms, synonyms and mutations of the sequence/structure vocabulary.
J Mol Biol. 175: 425-30, 1984.
[Journal]
492)  Nussinov R, Lennon GG.
Periodic structurally similar oligomers are found on one side of the axes of symmetry in the lac, trp, and gal operators.
J Biomol Struct Dyn. 2: 387-95, 1984.
[Journal]
493)  Nussinov R.
Promoter helical structure variation at the Escherichia coli polymerase interaction sites.
J Biol Chem. 259: 6798-805, 1984.
[Journal]
494)  Nussinov R.
Strong doublet preferences in nucleotide sequences and DNA geometry.
J Mol Evol. 20: 111-9, 1984.
[Journal]
495)  Nussinov R, Pieczenik G.
Structural and combinatorial constraints on base pairing in large nucleotide sequences.
J Theor Biol. 106: 245-59, 1984.
[Journal]
496)  Nussinov R, Lennon GG.
Structural features are as important as sequence homologies in Drosophila heat shock gene upstream regions.
J Mol Evol. 20: 106-10, 1984.
[Journal]
497)  Nussinov R.
An efficient code searching for sequence homology and DNA duplication.
J Theor Biol. 100: 319-28, 1983.
[Journal]
498)  Nussinov R.
Efficient algorithms for searching for exact repetition of nucleotide sequences.
J Mol Evol. 19: 283-5, 1983.
[Journal]
499)  Nussinov R.
RNA folding is unaffected by the nonrandom degenerate codon choice.
Biochim Biophys Acta. 698: 111-5, 1982.
[Journal]
500)  Nussinov R, Tinoco I, Jacobson AB.
Secondary structure model for the complete simian virus 50 late precursor mRNA.
Nucleic Acids Res. 10: 351-63, 1982.
[Journal]
501)  Nussinov R, Tinoco I, Jacobson AB.
Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.
Nucleic Acids Res. 10: 341-9, 1982.
[Journal]
502)  Nussinov R.
Some indications for inverse DNA duplication.
J Theor Biol. 95: 783-91, 1982.
[Journal]
503)  Nussinov R.
Splicing and transport of eukaryotic mRNAs: a theoretical model.
J Theor Biol. 97: 129-40, 1982.
[Journal]
504)  Nussinov R.
Balaban R, eds.
Nearest neighbor patterns in the DNA language. In: Structural Aspects of Recognition and Assembly in Biological Macromolecules.
Philadelphia : Glenside, Pa: Rehovot; 1981. p. 537-50 [Book Chapter]
505)  Wain-Hobson S, Brown RJ, Nussinov R.
Balaban M, eds.
The multiple coding capacity of DNA. In: Structural Aspects of Recognition and Assembly in Biological Macromolecules.
Philadelphia : Glenside, Pa: Rehovot; 1981. p. 551 [Book Chapter]
506)  Nussinov R.
Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage.
J Mol Biol. 149: 125-31, 1981.
[Journal]
507)  Nussinov R.
Nearest neighbor nucleotide patterns. Structural and biological implications.
J Biol Chem. 256: 8458-62, 1981.
[Journal]
508)  Wain-Hobson S, Nussinov R, Brown RJ, Sussman JL.
Preferential codon usage in genes.
Gene. 13: 355-64, 1981.
[Journal]
509)  Nussinov R, Tinoco I.
Sequential folding of a messenger RNA molecule.
J Mol Biol. 151: 519-33, 1981.
[Journal]
510)  Nussinov R.
The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice.
J Mol Evol. 17: 237-44, 1981.
[Journal]
511)  Nussinov R, Jacobson AB.
Fast algorithm for predicting the secondary structure of single-stranded RNA.
Proc Natl Acad Sci U S A. 77: 6903-13, 1980.
[Journal]
512)  Nussinov R, Sussman JL, Trifonov EN.
MS2 RNA has a potential to form an unusually large number of stable hairpins.
J Theor Biol. 85: 481-6, 1980.
[Journal]
513)  Nussinov R.
Some rules in the ordering of nucleotides in the DNA.
Nucleic Acids Res. 8: 4545-62, 1980.
[Journal]
514)  Nussinov R.
Strong adenine clustering in nucleotide sequences.
J Theor Biol. 85: 285-91, 1980.
[Journal]
515)  Nussinov R.
Three dimensional structure and sequence homology determine splicing sites in eukaryotic precursor RNA.
J Theor Biol. 83: 647-62, 1980.
[Journal]
516)  Nussinov R, Pieczenik G, Griggs J, Kleitman D.
Algorithms for loop matchings.
Soc. Ind. Appl. Math. 35: 68-82, 1978.
[Journal]
Click Here to View Collapsed Bibliography.

This page was last updated on 12/11/2013.