TASSER: An automated method for the prediction of protein tertiary structures in CASP6

Proteins: Structure, Function and Genetics

Volumn 61, Issue SUPPL. 7, 2005, Pages 91-98

  Zhang, Yang ^a   Arakaki, Adrian K ^a   Skolnick, Jeffrey ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Ab initio prediction; Comparative modeling; PROSPECTOR_3; TASSER; Threading

Indexed keywords

AB INITIO CALCULATION; ANALYTIC METHOD; AUTOMATION; CONFERENCE PAPER; CRITICAL ASSESSMENT OF PROTEIN STRUCTURE PREDICTION METHOD; MOLECULAR RECOGNITION; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN TARGETING; PROTEIN TERTIARY STRUCTURE; SAMPLING; STRUCTURE ANALYSIS;

ALGORITHMS; AUTOMATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; COMPUTERS; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 30344488120     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20724     Document Type: Conference Paper

References (31)

1. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins 2001;Suppl 5:2-7.
2. Moult J, Fidelis K, Zemla A, Hubbard T. Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins 2003;53(Suppl 6):334-339.
3. Pillardy J, Czaplewski C, Liwo A, Lee J, Ripoll DR, Kazmierkiewicz R, Oldziej S, Wedemeyer WJ, Gibson KD, Arnautova YA, Saunders J, Ye YJ, Scheraga HA. Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proc Natl Acad Sci USA 2001;98:2329-2333.
4. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
5. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003;85:1145-1164.
6. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
7. Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
8. Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
9. Tramontane A, Morea V. Assessment of homology-based predictions in CASP5. Proteins 2003;53(Suppl 6):352-368.
10. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
11. Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
12. Murzin AG, Bateman A. CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4. Proteins 2001;Suppl 5:76-85.
13. Ginalski K, Rychlewski L. Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins 2003;53(Suppl 6):410-417.
14. Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
15. Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
16. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
17. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004;56:502-518.
18. Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 2004;87:2647-2655.
19. Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 2005;102:1029-1034.
20. Zhang Y, Skolnick J. Structure modeling of 907 G protein-coupled receptors in the human genome. 2004. Submitted for publication.
21. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
22. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
23. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
24. Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002;48:192-201.
25. Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL III. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins 2000;41:86-97.
26. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on TM-score. Nucl Acid Res 2005;77(7):2302-2309.
27. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
28. Kihara D, Skolnick J. The PDB is a covering set of small protein structures. J Mol Biol 2003;334:793-802.
29. Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics 2004;20:1087-1096.
30. Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilagyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins 2003;53(Suppl 6):469-479.
31. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR-a new approach to threading. Proteins 2001;42:319-331.