A study of quality measures for protein threading models

BMC Bioinformatics

Volumn 2, Issue , 2001, Pages

  Cristobal, Susana ^a   Zemla, Adam ^b   Fischer, Daniel ^c   Rychlewski, Leszek ^d   Elofsson, Arne ^e  

^a UPPSALA UNIVERSITY   (Sweden)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^c BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^d INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^e STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; INTERMETHOD COMPARISON; MODEL; MOLECULAR BIOLOGY; PREDICTION; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE; QUALITY CONTROL; REPRODUCIBILITY; SCORING SYSTEM; SEQUENCE ALIGNMENT; BIOLOGY; CHEMICAL STRUCTURE; COMPARATIVE STUDY; EVALUATION; GENETICS; METHODOLOGY; PREDICTION AND FORECASTING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; STANDARD; STATISTICS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PREDICTIVE VALUE OF TESTS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 0642373240     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-2-5     Document Type: Article

References (31)

1. Moult J, Hubbard T, Bryant SH, Fidelis K, Pedersen JT: Critical assesment of methods of proteins structure predictions (CASP): Round II. Proteins. Proteins: Struct. Funct. Genet. 1997,Suppl 1:2-6
2. Fisher D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus K, Kelley L, MacCallum R, Pawowski K, Rost B, Rychlewski L, Sternberg M: Critical assesment of methods of proteins structure predictions (CASP): Round II. Proteins: Struct. Funct. Genet. 1999, Suppl 3:209-217
3. Murzin A: Structure classification-based assessment of casp3 predictions for the fold recognition targets. Proteins: Struct. Funct. Genet. 1999, Suppl 3:88-103
4. .Abagyan RA, Batalov S: Do aligned sequences share the same fold? J. Mol. Biol. 1997, 273:355-368
5. Brenner SE, C C, Hubbard T: Assessing sequence comparison methods with reliable structurally identified evolutionary relationships. Proc. Natl. Acad. Sci. USA 1998, 95:6073-6078
6. Park J, Teichmann SA, Hubbard T, Chothia C: Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol. 1997, 273:249-254
7. Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, C C: Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 1998, 284:1201-1210
8. Fischer D, Eisenberg D: Protein fold recognition using sequence-derived predictions. Protein Sci. 1996, 5:947-955
9. Rice D, Eisenberg D: A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol. 1997, 267:1026-1038
10. Di Francesco V, Geetha V, Garnier J, Munson PJ: Fold recognition using predicted secondary structure sequences and hidden Markov models of proteins folds. Proteins: Struct. Funct. Genet., 1997, Suppl 1:123-128
11. Rost B, Schneider R, Sander C: Protein fold recognition by prediction- based threading. J. Mol. Biol. 1997, 270:471-480
12. Hargbo J, Elofsson A: A study of hidden markov models that use predicted secondary structures for fold recognition. Proteins: Struct. Funct. Genet. 1999, 36:68-87
13. Lindahl E, Elofsson A: Identification of related proteins on family, superfamily and fold level. J. Mol. Biol. 2000, 295:613-625
14. Domingues F, Lackner P, Andreeva A, Sippl MJ: Structure based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol 2000, 297(4):1003-1013
15. Marchler-Bauer A, Bryant S: A measure of progress in fold recognition? Proteins: Struct. Funct. Genet. 1999, Suppl 3:218-225
16. Elofsson A: A study on how to best align protein sequences. Proteins: Struct. Funct. Genet. 2000
17. Bujnicki J, Elofsson A, Fischer D, Rychlewski L: Livebench: Continous benchmarking of protein structure prediction servers. Protein Science 2001, 10(2):352-361
18. Marchler-Bauer A, Bryant S: Measures of threading specificity and accuracy? Proteins: Struct. Funct. Genet. 1997, Suppl 2:74-82
19. Zemla A, Venclovas C, Reinhardt A, Fidelis KTJH: Numerical criteria for the evaluation of ab initio predictions of protein structure. Proteins: Struct. Funct. Genet. 1997, Suppl 1:140-150
20. Zemla A, Venclovas C, Moult J, Fidelis K: Processing and analysis of casp3 protein structure predictions. Struct. Funct. Genet. 1999, Suppl 3:22-29
21. Lackner P, Koppensteiner W, Domingues F, Sippl M: Automated large scale evaluation of protein structure predictions. Proteins: Struct. Funct. Genet. 1999, Suppl 3:7-14
22. Siew N, Elofsson A, Rychlewski L, Fischer D: Maxsub: An automated measure to assess the quality of protein structure predictions. Bionformatics 2000, 16(9):776-785
23. Levitt M, Gerstein M: A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A 1998, 95(11):5913-20
24. Hubbard T: Rmsd/coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions. Proteins: Struct. Funct. Genet. 1999, Suppl 3:15-21
25. Feng ZK, Sippl M: Optimum superimposition of protein structures, ambiguities and implications. Fold. Des. 1996, 1:123-132
26. Holm L, Sander C: Touring protein fold space with dali/fssp. Nucl. Acid. Res. 1998, 26:316-319
27. Gibrat J, Madej T, Bryant S: Surprising similarities in structure comparison. Current Opinion in Structural Biology 1996, 6:377-385
28. Murzin AG, Brenner SE, Hubbard T, Chothia C: Scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247:536-54
29. Abagyan R, Totrov M: Contact area difference (cad): a robust measure to evaluate accuracy of protein models. J. Mol. Biol 1997, 268(3):678-685
30. Jones T, Kleywegt G: Casp3 comperative modeling evaluation. Proteins: Struct. Funct. Genet. 1999, Suppl 3:30-47
31. Orengo C, Bray J, Hubbard T, LoConte L, Sillitoe I: Analysis and assessment of ab initio three-dimensional prediction, secondary structure and contacts predictions. Proteins: Struct. Funct. Genet. 1999, Suppl 3:149-171