Performance of the Pro-sp3-TASSER server in CASPB

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue SUPPL. 9, 2009, Pages 123-127

  Zhou, Hongyi ^a   Pandit, Shashi B ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Chunk TASSER; Protein structure prediction; TASSER

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TARGETING; QUALITY CONTROL; SCORING SYSTEM; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; METHODOLOGY; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 74249095557     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22501     Document Type: Article

References (17)

1. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on genomic scale. Proc Natl Acad Sci USA. 2004; 101: 7594-7599. (Pubitemid 38658074)
2. Zhou H, Skolnick J. Ab initio protein structure prediction using chunk-TASSER. Biophys J 2007; 93: 1510-1518. (Pubitemid 47403296)
3. Zhang Y, Arakaki A, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005; 61: 91-98. (Pubitemid 43069961)
4. Zhang Y, Devries ME, Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol 2006; 2: 0088-0099.
5. Pandit SB, Zhang Y, Skolnick J. TASSER-lite: an automated tool for protein comparative modeling. Biophys J 2006; 91: 4180-4190. (Pubitemid 44887276)
6. Zhou H, Pandit SB, Lee S, Borreguerro J, Chen H, Wroblewska L, Skolnick J. Analysis of TASSER, based CASP7 protein structure prediction results. Proteins 2007; 69: 90-97. (Pubitemid 350210116)
7. Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004; 55: 1005-1013. (Pubitemid 38702957)
8. Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005; 58: 321-328. (Pubitemid 40076048)
9. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004; 56: 502-518. (Pubitemid 38924963)
10. Lee S, Skolnick J. Benchmarking of TASSER-2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J 2008; 95: 1956-1964.
11. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-jury: a simple approach to improve protein structure predictions. Bioinformatics 2003; 19: 1015-1018. (Pubitemid 36675823)
12. Zhou H, Skolnick J. Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential. Proteins 2007; 71: 1211-1218. (Pubitemid 351564047)
13. Zhou H, Skolnick J. Protein structure prediction by pro-sp3TASSER. Biophys J 2009; 96: 2119-2127.
14. Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res 2006; 34: e112. (Pubitemid 44605642)
15. Rotkiewicz P, Skolnick J. Fast procedure for reconstruction of fullatom protein models from reduced representations. J Comput Chem 2008; 29: 1460-1465. (Pubitemid 351757769)
16. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 2002; 11: 2714-2726. (Pubitemid 35191145)
17. Zhang Y, Skolnick J. A scoring function for the automated, assessment of protein structure template quality. Proteins 2004; 57: 702-710. (Pubitemid 39626992)