CASP6 assessment of contact prediction

Proteins: Structure, Function and Genetics

Volumn 61, Issue SUPPL. 7, 2005, Pages 214-224

  Graña, Osvaldo ^a   Baker, David ^b   MacCallum, Robert M ^c   Meiler, Jens ^d   Punta, Marco ^e   Rost, Burkhard ^e   Tress, Michael L ^a   Valencia, Alfonso ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e CUBIC   (United States)

Author keywords

CASP6 assessment; Contact prediction evaluation; Interresidue distances

Indexed keywords

ACCURACY; ANALYTIC METHOD; CASP6 SYSTEM; COMPUTER PREDICTION; COMPUTER SYSTEM; CONFERENCE PAPER; EVALUATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

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

EID: 30344453347     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20739     Document Type: Conference Paper

References (52)

1. Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241.
2. Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
3. Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins Suppl 1999;3:177-185.
4. Altschuh D, Lesk AM, Bloomer AC, Klug A. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 1987;193:693-707.
5. Altschuh D, Vernet T, Berti P, Moras D, Nagai K. Coordinated amino acid changes in homologous protein families. Protein Eng 1988;2:193-199.
6. Shindyalov IN, Kolchanov NA, Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994;7:349-358.
7. Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.
8. Taylor WR, Hatrick K. Compensating changes in protein multiple sequence alignments. Protein Eng 1994;7:341-348.
9. Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des Suppl 1997;2:25-32.
10. Lapedes AS, Giraud BG, Liu LC, Stormo GD. Correlated mutations in protein sequences: phylogenetic and structural effects. PASCSMB 1997;1-22.
11. Chelvanayagam G, Eggenschwiler A, Knecht L, Gonnet GH, Benner SA. An analysis of simultaneous variation in protein structures. Protein Eng 1997;10:307-316.
12. Dekker JP, Fodor A, Aldrich RW, Yellen G. A perturbation-based method for calculating explicit likelihood of evolutionary covariance in multiple sequence alignments. Bioinformatics 2004;20: 1565-1572.
13. Zhang C, Hou J, Kim SH. Fold prediction of helical proteins using torsion angle dynamics and predicted restraints. Proc Natl Acad Sci USA 2002;99:3581-3585.
14. Zhu J, Zhu Q, Shi Y, Liu H. How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins 2003;52:598-608.
15. Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001;14:835-843.
16. Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins Suppl 2001;5:157-162.
17. Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics Suppl 2002;18:62-70.
18. Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins Suppl 2003;53:497-502.
19. Vullo A, Frasconi P. Prediction of protein coarse contact maps. J Bioinform Comput Biol 2003;1:411-431.
20. MacCallum RM. Striped sheets and protein contact prediction. Bioinformatics Suppl 2004;20:224-231.
21. Gupta N, Mangal N, Biswas S. Evolution and similarity evaluation of protein structures in contact map space. Proteins 2005;59: 196-204.
22. Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics 2005;21:2960-2968.
23. Lesk AM. CASP2: Report on ab initio predictions. Proteins Suppl 1997;1:151-166.
24. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins Suppl 1999;3:149-170.
25. Lesk AM, Lo Conte L, Hubbard T. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins Suppl 2001;5:98-118.
26. Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins Suppl 2003;6:436-456.
27. Dunbrack et al. Targets. Proteins 2005;Suppl 7:8-18.
28. Fischer D, Elofsson A, Rychlewski L, Pazos F, Valencia A, Rost B, Ortiz AR, Dunbrack RL Jr. CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins Suppl 2001;5:171-183.
29. Eyrich VA, Przybylski D, Koh IY, Grana O, Pazos F, Valencia A, Rost B. CAFASP3 in the spotlight of EVA. Proteins Suppl 2003;6:548-560.
30. Grana O, Evrich VA, Pazos F, Rost B, Valencia A. EVAcon: a protein contact prediction evaluation service. Nucleic Acid Res 2005;33(Web Server issue):W347-W351.
31. Holm L, Sander C. Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol 1991;218:183-194.
32. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein-protein interaction. J Mol Biol 1997;271:511-523.
33. Altschul SF, Madden TL, Scharfer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
34. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Peons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
35. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
36. 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.
37. Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Sci 2002;11:1937-1944.
38. Bradley P, Baker D. Rosetta in CASP6. in prep.
39. Rychlewski L, Fischer D. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci 2005;14:240-245.
40. Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA 2003;100:12105-12110.
41. Meiler J, Müller M, Zeidler A, Schmäschke F. Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks. J Mol Model 2001;7:360-369.
42. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
43. Rost B. PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 1996;266:525-539.
44. Rost B, Yachdav G, Liu J. The Predict Protein server. Nucleic Acids Res Suppl 2004;32:321-326.
45. Rost B. Protein secondary structure prediction continues to rise. J Struc Biol 2001;134:204-218.
46. Rost B. How to use protein ID structure predicted by PROFphd. In: Walker JE, editor. The proteomics protocols handbook, methods in molecular biology. Totowa NJ: Humana 2005. p 875-901.
47. Creighton T. Proteins: structures and molecular properties. New York: Company WHFa; 1992.
48. Wootton JC, Federhen S. Analysis of compositionally biased regions in sequence databases. Methods Enzymol 1996;266:554-571.
49. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res Suppl 2004;32: 226-229.
50. Punta M, Rost B. Protein folding rates estimated from contact predictions. J Mol Biol 2005;348:507-512.
51. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Pagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002;58:899-907.
52. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:27-28.