Title:
Application of sparse NMR restraints to large-scale protein structure prediction

Simple item page
dc.contributor.author Li, Wei
dc.contributor.author Zhang Yang
dc.contributor.author Skolnick, Jeffrey
dc.contributor.corporatename Georgia Institute of Technology. Center for the Study of Systems Biology
dc.contributor.corporatename Georgia Institute of Technology. School of Biology
dc.contributor.corporatename State University of New York at Buffalo. Center of Excellence in Bioinformatics
dc.date.accessioned 2011-11-08T20:58:50Z
dc.date.available 2011-11-08T20:58:50Z
dc.date.issued 2004-08
dc.description © 2004 by the Biophysical Society en_US
dc.description.abstract The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated as follows: First, a representative benchmark set of the Protein Data Bank library consisting of 1365 proteins up to 200 residues was employed. Using N/8 simulated long-range restraints, where N is the number of residues, 1023 (75%) proteins were folded to a Ca root-mean-square deviation (RMSD) from native ,6.5A˚ in one of the top five models. The average RMSD of the models for all 1365 proteins is 5.0 A˚ . Using N/4 simulated restraints, 1206 (88%) proteins were folded to a RMSD ,6.5 A˚ and the average RMSD improved to 4.1 A˚ . Then, 69 proteins with experimental NMR data were used. Using long-range NOE-derived restraints, 47 proteins were folded to a RMSD ,6.5 A˚ with N/8 restraints and 61 proteins were folded to a RMSD ,6.5 A˚ with N/4 restraints. Thus, TOUCHSTONEX can be a tool for NMR-based rapid structure determination, as well as used in other experimental methods that can provide tertiary restraint information. en
dc.identifier.citation Li, W, Zhang Y, Skolnick J. 2004. Application of sparse NMR restraints to large-scale protein structure prediction. Biophysical journal. 87(2):1241-8. en
dc.identifier.issn 0006-3495
dc.identifier.uri http://hdl.handle.net/1853/41963
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.publisher.original Biophysical Society
dc.subject Protein structure prediction algorithm en
dc.subject TOUCHSTONEX en
dc.subject Nuclear Overhauser enhancement en
dc.subject Root-mean-square deviation from native en
dc.subject Benchmark protein set en
dc.title Application of sparse NMR restraints to large-scale protein structure prediction en_US
dc.type Text
dc.type.genre Article
dspace.entity.type Publication
local.contributor.author Skolnick, Jeffrey
local.contributor.corporatename College of Sciences
local.contributor.corporatename School of Biological Sciences
local.contributor.corporatename Center for the Study of Systems Biology
relation.isAuthorOfPublication 80f29357-f18b-4635-abd1-628d627d301d
relation.isOrgUnitOfPublication 85042be6-2d68-4e07-b384-e1f908fae48a
relation.isOrgUnitOfPublication c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5
relation.isOrgUnitOfPublication d3d635bd-b38e-4ef6-a2d0-0875b9a83e34
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
CSSB_BJ_2004_001.pdf
Size:
150.11 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Research Publications