A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction

Current Opinion in Structural Biology

Volumn 15, Issue 3 SPEC. ISS., 2005, Pages 285-289

  Moult, John ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; TRANSFER RNA;

AMINO ACID SEQUENCE; BETA SHEET; ENZYME SPECIFICITY; EVOLUTIONARY HOMOLOGY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PROTEIN TARGETING; REVIEW; STRUCTURE ANALYSIS;

EID: 20444484434     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.05.011     Document Type: Review

References (35)

1. P.E. Bourne CASP and CAFASP experiments and their findings Methods Biochem Anal 44 2003 501 507 An independent review of the state of the art in protein structure modeling.
2. A. Zemla, Venclovas, J. Moult, and K. Fidelis Processing and evaluation of predictions in CASP4 Proteins suppl 5 2001 13 21
3. A. Tramontano, and V. Morea Assessment of homology-based predictions in CASP5 Proteins 53 suppl 6 2003 352 368 An assessment of the state of the art in comparative modeling of protein structure.
4. L.N. Kinch, J.O. Wrabl, S.S. Krishna, I. Majumdar, R.I. Sadreyev, Y. Qi, J. Pei, H. Cheng, and N.V. Grishin CASP5 assessment of fold recognition target predictions Proteins 53 suppl 6 2003 395 409 An assessment of the state of the art in fold-recognition-based modeling.
5. P. Aloy, A. Stark, C. Hadley, and R.B. Russell Predictions without templates: new folds, secondary structure, and contacts in CASP5 Proteins 53 suppl 6 2003 436 456 An assessment of the state of the art in template-free modeling.
6. C. Venclovas, A. Zemla, K. Fidelis, and J. Moult Assessment of progress over the CASP experiments Proteins 53 suppl 6 2003 585 595 An analysis of progress over the course of the CASP experiments.
7. S.Y. Chung, and S. Subbiah The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins Protein Sci 4 1995 2300 2309
8. S. An, and K. Musier-Forsyth Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein J Biol Chem 279 2004 42359 42362
9. C. DeWeese-Scott, and J. Moult Molecular modeling of protein function regions Proteins 55 2004 942 961 An analysis of the usefulness of comparative modeling in interpreting details of molecular function.
10. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 1997 3389 3402
11. K. Karplus, and B. Hu Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set Bioinformatics 17 2001 713 720
12. K. Karplus, C. Barrett, and R. Hughey Hidden Markov models for detecting remote protein homologies Bioinformatics 14 1998 846 856
13. Kahsay RY, Wang G, Gao G, Liao L, Dunbrack R: Quasi-consensus based comparison of profile hidden Markov models for protein sequences. Bioinformatics 2005, doi:10.1093/bioinformatics/bti374.
14. T. Ohlson, B. Wallner, and A. Elofsson Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods Proteins 57 2004 188 197 An evaluation of profile-profile alignment methods.
15. G. Wang, and RL. Dunbrack Jr. Scoring profile-to-profile sequence alignments Protein Sci 13 2004 1612 1626
16. B. Wallner, H. Fang, T. Ohlson, J. Frey-Skott, and A. Elofsson Using evolutionary information for the query and target improves fold recognition Proteins 54 2004 342 350
17. M.A. Marti-Renom, M.S. Madhusudhan, and A. Sali Alignment of protein sequences by their profiles Protein Sci 13 2004 1071 1087
18. P.A. Bates, L.A. Kelley, R.M. MacCallum, and M.J. Sternberg Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM Proteins suppl 5 2001 39 46
19. J.O. Wrabl, and N.V. Grishin Gaps in structurally similar proteins: towards improvement of multiple sequence alignment Proteins 54 2004 71 87
20. L.J. McGuffin, and D.T. Jones Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 19 2003 874 881
21. D. Przybylski, and B. Rost Improving fold recognition without folds J Mol Biol 341 2004 255 269
22. K. Karplus, R. Karchin, J. Draper, J. Casper, Y. Mandel-Gutfreund, M. Diekhans, and R. Hughey Combining local-structure, fold-recognition, and new fold methods for protein structure prediction Proteins 53 suppl 6 2003 491 496
23. M. von Grotthuss, J. Pas, L. Wyrwicz, K. Ginalski, and L. Rychlewski Application of 3D-Jury, GRDB, and Verify3D in fold recognition Proteins 53 suppl 6 2003 418 423
24. M.J. Sippl Recognition of errors in three-dimensional structures of proteins Proteins 17 1993 355 362
25. C. Venclovas Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance Proteins 53 suppl 6 2003 380 388
26. L. Rychlewski, and D. Fischer LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction Protein Sci 14 2005 240 245 A report on the performance of servers for protein structure modeling, including metaservers.
27. A. Godzik Fold recognition methods Methods Biochem Anal 44 2003 525 546
28. J. Skolnick, Y. Zhang, A.K. Arakaki, A. Kolinski, M. Boniecki, A. Szilagyi, and D. Kihara TOUCHSTONE: a unified approach to protein structure prediction Proteins 53 suppl 6 2003 469 479
29. A.F. Coulson, and J. Moult A unifold, mesofold, and superfold model of protein fold use Proteins 46 2002 61 71
30. P. Du, M. Andrec, and R.M. Levy Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update Protein Eng 16 2003 407 414
31. C. Bystroff, Y. Shao, and X. Yuan Five hierarchical levels of sequence-structure correlation in proteins Appl Bioinformatics 3 2004 97 104
32. C.A. Rohl, C.E. Strauss, K.M. Misura, and D. Baker Protein structure prediction using Rosetta Methods Enzymol 383 2004 66 93 A detailed description of one of the more successful packages for template-free modeling of protein structure.
33. D.T. Jones, and L.J. McGuffin Assembling novel protein folds from super-secondary structural fragments Proteins 53 suppl 6 2003 480 485
34. C. Bystroff, K.T. Simons, K.F. Han, and D. Baker Local sequence-structure correlations in proteins Curr Opin Biotechnol 7 1996 417 421
35. J. Skolnick, A. Kolinski, D. Kihara, M. Betancourt, P. Rotkiewicz, and M. Boniecki Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement Proteins suppl 5 2001 149 156