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Our Science – Wang Website

Yun-Xing Wang, Ph.D.

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•  The 3P program package - "3P" stands for periodicity, planarity, and pixel. The 3P program is based on the intrinsic periodic correlations between residual dipolar couplings (RDCs) and in-plane internuclear vectors, and between RDCs and the orientation of peptide planes relative to an alignment tensor. The program extracts accurate rhombic, axial components of the alignment tensor without explicit coordinates, and discrete peptide plane orientations, which are utilized in combination with readily available phi/psi angles to determine the three-dimensional backbone structures of proteins. The 3P program uses one alignment tensor. The package includes the detailed examples that demonstrate the utility and robustness of the program, using both experimental and synthetic data sets, which were added with different levels of noise or were incomplete. The output of the program is interfaced to Xplor-NIH ( J Magn Reson. 2007 Nov;189(1):90-103.)
•  Refining protein structures with the Small Angle Neutron Scattering data and NMR restraints (1) - While the restraints of residual dipolar couplings (RDCs) define the relative orientations among domains of multi-domain proteins, the relative positioning among the domains is under-defined, when few inter-domain NOE-distance restraints are available. Since the Small Angle X-ray/Neutron Scattering data contains the information about the global shape of a protein, we developed a protocol to refine protein structures with the restraint of the Small Angle Neutron Scattering (SANS) data, in addition to distance, dihedral and RDC restraints. This protocol is demonstrated in determining the structure of ribosome protein L11 [Lee, al. The Structure of Free L11 and Functional Dynamics of L11 in Free, L11-rRNA(58 nt) Binary and L11-rRNA(58 nt)-thiostrepton Ternary Complexes. J. Mol. Biol., 367(4), 1007-1022, 2007.]. This link contains the Xplor-nih protocol that used for the refinement calculation.
•  Define interface in a homodimeric RNA:RNA complex and refine the global structure - Please click the link above to go to the site for download of the rigid-body calculation protocols for a RNA:RNA complex (J Am Chem Soc. 2008 Mar 19;130(11):3292-3).
•  GASR program and protocol downloads - The GASR program can be downloaded, together with all testing examples and the Xplor-NIH calculation protocols.
GASR-Xplor-NIH-protocols.tar: contains all Xplor-NIH protocols used in the GASR paper (J. Am. Chem. Soc., 2009, 131 (30), pp 10507-10515);
GASR-v1.0.tgz: the GASR program itself.
•  G2G - G2G is a toolbox used for generating global structures of RNAs using NMR and SAXS data. For details, please see reference: J Mol Biol. 2009 Aug 8. PMID: 19666030.
•  The 1st NIH Workshop on Small Angle X-ray Scattering and Application in Biomolecular Studies - The lecture notes for the First NIH Workshop on Small Angle X-ray Scattering and Application in Biomolecular Studies can be downloaded from this link.
•  The sample preparation protocol for SAXS - This link contains explicit instructions for sample and buffer solution preparation.
•  The Cairns ICMRBS SAXS-SANS-NMR Workshop (Combined Small Angle X-ray and Neutron Scattering with Bio - The Cairns ICMRBS workshop announcement
•  All Downloads - This is an alternate download page for all downloads. All of other links above may or may not work from time to time.

This page was last updated on 7/19/2011.