Analysis of TASSER-based CASP7 protein structure prediction results.

Analysis of TASSER-based CASP7 protein structure prediction results. Research Abstract Details 

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Analysis of TASSER-based CASP7 protein structure prediction results. Abstract Text:

Hongyi Zhou,Shashi B Pandit,Seung Yup Lee,Jose Borreguero,Huiling Chen,Liliana Wroblewska,Jeffrey Skolnick,Hongyi Zhou,Shashi B Pandit,Seung Yup Lee,Jose Borreguero,Huiling Chen,Liliana Wroblewska,Jeffrey Skolnick,

An improved TASSER (Threading/ASSEmbly/Refinement) methodology is applied to predict the tertiary structure for all CASP7 targets. TASSER employs template identification by threading, followed by tertiary structure assembly by rearranging continuous template fragments, where conformational space is searched via Parallel Hyperbolic Monte Carlo sampling with an optimized force-field that includes knowledge-based statistical potentials and restraints derived from threading templates. The final models are selected by clustering structures from the low temperature replicas. Improvements in TASSER over CASP6 involve use of better templates from 3D-jury applied to three threading programs, PROSPECTOR_3, SP(3), and SPARKS, and a fragment comparison method for better model ranking. For targets with no reliable templates, a variant of TASSER (chunk-TASSER) is also applied with potentials and restraints extracted from ab initio folded supersecondary chunks of the target to build full-length models. For all 124 CASP targets/domains, the average root-mean-square-deviation (RMSD) from native and alignment coverage of the best initial threading models from 3D-jury are 6.2 A and 93%, respectively. Following TASSER reassembly, the average RMSD of the best model in the template aligned region decreases to 4.9 A and the average TM-score increases from 0.617 for the template to 0.678 for the best full-length model. Based on target difficulty, the average TM-scores of the final model to native are 0.904, 0.671, and 0.307 for high-accuracy template-based modeling, template-based modeling, and free modeling targets/domains, respectively. For the more difficult targets, TASSER with modest human intervention performed better in comparison to its server counterpart, MetaTASSER, which used a limited time simulation.

Analysis of TASSER-based CASP7 protein structure prediction results. Publishing Authors By Initials

H Zhou,SB Pandit,SY Lee,J Borreguero,H Chen,L Wroblewska,J Skolnick,H Zhou,SB Pandit,SY Lee,J Borreguero,H Chen,L Wroblewska,J Skolnick,

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Analysis of TASSER-based CASP7 protein structure prediction results. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Proteins

VOLUME: 69 Suppl 8

Page Numbers: 90-7

Journal Abbreviation: Proteins

ISSN: 1097-0134

DAY: 27

MONTH: 11

YEAR: 2007

Analysis of TASSER-based CASP7 protein structure prediction results. Information

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LANGUAGE: eng

NlmUniqueID: 8700181

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Grant and Affiliation Information for Analysis of TASSER-based CASP7 protein structure prediction results.

AFFILIATION: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM-48835

ACRONYM: GM

MEDLINETA: Proteins

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