Title:
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

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dc.contributor.author Zhang, Yang
dc.contributor.author Skolnick, Jeffrey
dc.contributor.corporatename State University of New York at Buffalo. Center of Excellence in Bioinformatics
dc.date.accessioned 2011-10-31T19:45:13Z
dc.date.available 2011-10-31T19:45:13Z
dc.date.issued 2004-10
dc.description © 2004 by the Biophysical Society en_US
dc.description.abstract We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced Ca and side-chain based potential consistent with threading based tertiary restraints. Predictions were generated for 745 proteins 201– 300 residues in length that cover the Protein Data Bank (PDB) at the level of 35% sequence identity. With homologous proteins excluded, in 365 cases, the templates identified by our threading program, PROSPECTOR_3, have a root-mean-square deviation (RMSD) to native , 6.5 A˚ , with .70% alignment coverage. After TASSER assembly, in 408 cases the best of the top five full-length models has a RMSD , 6.5 A˚ . Among the 745 targets are 18 membrane proteins, with one-third having a predicted RMSD , 5.5 A˚ . For all representative proteins less than or equal to 300 residues that have corresponding multiple NMR structures in the Protein Data Bank, 20% of the models generated by TASSER are closer to the NMR structure centroid than the farthest individual NMR model. These results suggest that reasonable structure predictions for nonhomologous large size proteins can be automatically generated on a proteomic scale, and the application of this approach to structural as well as functional genomics represent promising applications of TASSER. en
dc.identifier.citation Zhang, Y, Skolnick J. 2004. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophysical journal. 87(4):2647-55. en
dc.identifier.issn 0006-3495
dc.identifier.uri http://hdl.handle.net/1853/41946
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.publisher.original Biophysical Society
dc.subject Tertiary structure predictions en
dc.subject TASSER en
dc.subject Algorithms en
dc.subject Protein structure modeling tool en
dc.title Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins en
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
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