A "FRankenstein's Monster" Approach to Comparative Modeling: Merging the Finest Fragments of Fold-Recognition Models and Iterative Model Refinement Aided by 3D Structure Evaluation

Proteins: Structure, Function and Genetics

Volumn 53, Issue SUPPL. 6, 2003, Pages 369-379

  Kosinski, Jan ^a   Cymerman, Iwona A ^a   Feder, Marcin ^a   Kurowski, Michal A ^a   Sasin, Joanna M ^a   Bujnicki, Janusz M ^a  

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

Author keywords

Bioinformatics; Consensus generation; GeneSilico; Homology modeling; Model evaluation

Indexed keywords

AB INITIO CALCULATION; AUTOMATION; BIOINFORMATICS; CATALYSIS; CONFERENCE PAPER; GENE DELETION; GENE INSERTION; HUMAN; INTERNET; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STEREOCHEMISTRY; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

ALGORITHMS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 0242362160     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10545     Document Type: Conference Paper

References (33)

1. Venclovas Zemla A, Fidelis K, Moult J. Comparison of performance in successive CASP experiments. Proteins 2001;45 Suppl 5:163-70 2001;45 Suppl 5:163-170.
2. 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 2001;45 Suppl 5:171-183.
3. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-2: Large-scale automated evaluation of protein structure prediction servers. Proteins 2001;45:184-191.
4. Tramontano A, Leplae R, Morea V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins 2001;45 Suppl 5:22-38.
5. Sippl MJ, Lackner P, Domingues FS, Prlic A, Malik R, Andreeva A, Wiederstein M. Assessment of the CASP4 fold recognition category. Proteins 2001;45 Suppl 5:55-67.
6. Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M, Grate L, Casper J, Hughey R. What is the value added by human intervention in protein structure prediction? Proteins 2001;45 Suppl 5:86-91.
7. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995;20:374-376.
8. LoConte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res 2000;28:257-259.
9. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Structure prediction Meta Server. Bioinformatics 2001;17:750-751.
10. Douguet D, Labesse G. Easier threading through web-based comparisons and cross-validations. Bioinformatics 2001;17:752-753.
11. Rost B. Predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 1996;266:525-539.
12. Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003;31:3305-3307.
13. Kelley LA, McCallum CM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:501-522.
14. Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000;119-130.
15. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
16. Shi J, Blundell TL, Mizuguchi K. Fugue: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310: 243-257.
17. Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287: 797-815.
18. Xu J, Li M, Lin G, Kim D, Xu Y. Protein structure prediction by linear programming. Pac Symp Biocomput 2003;in press
19. Altschul SF, Madden TL, Schaffer 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.
20. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876-4882.
21. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
22. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
23. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
24. Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF. The GROMOS biomolecular simulation program package. J Phys Chem 1999;103:3596-3607.
25. Dunbrack RL. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Proteins 1999;Suppl 3:81-87.
26. Cuff JA, Barton GJ. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000;40:502-511.
27. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
28. Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002;47:228-235.
29. Ouali M, King RD. Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000;9:1162-1176.
30. Bujnicki JM. Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol 1999;1:1-8, http://www.bioinfo.de/isb/1999-01/0016/.
31. 1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett 2001;507: 123-127.
32. Aravind L, Koonin EV. DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res 1999;27:1609-1618.
33. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins 2001;45 Suppl 5:119-126.