Title:
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints
dc.contributor.author | Lee, Seung Yup | |
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.date.accessioned | 2011-10-28T19:33:30Z | |
dc.date.available | 2011-10-28T19:33:30Z | |
dc.date.issued | 2008-08 | |
dc.description | © 2008 by the Biophysical Society | en_US |
dc.description.abstract | To improve tertiary structure predictions of more difficult targets, the next generation of TASSER, TASSER_2.0, has been developed. TASSER_2.0 incorporates more accurate side-chain contact restraint predictions from a new approach, the composite-sequence method, based on consensus restraints generated by an improved threading algorithm, PROSPECTOR_3.5, which uses computationally evolved and wild-type template sequences as input. TASSER_2.0 was tested on a large-scale, benchmark set of 2591 nonhomologous, single domain proteins " 200 residues that cover the Protein Data Bank at 35% pairwise sequence identity. Compared with the average fraction of accurately predicted side-chain contacts of 0.37 using PROSPECTOR_3.5 with wildtype template sequences, the average accuracy of the composite-sequence method increases to 0.60. The resulting TASSER_2.0 models are closerto their native structures, with an average root mean-square deviation of 4.99 A compared to the 5.31 A result of TASSER. Defining a successful prediction as a model with a root mean-square deviation to native < 6.5 A. the success rate of TASSER_2.0 (TASSER) for Medium targets (targets with good templates/poor alignments) is 74.3% (64.7%) and 40.8% (35.5%) for the Hard targets (incorrect templates/alignments). For Easy targets (good templates/alignments), the success rate slightly increases from 86.3% to 88.4% | en |
dc.identifier.citation | Lee, SY, Skolnick J. 2008. Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophysical journal. 95(4):1956-64. | en |
dc.identifier.issn | 0006-3495 | |
dc.identifier.uri | http://hdl.handle.net/1853/41937 | |
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 2.0 | en |
dc.subject | Protein structure prediction algorithm | en |
dc.title | Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints | 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 | |
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 |
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