fams-ace: A combined method to select the best model after remodeling all server models

Proteins: Structure, Function and Genetics

Volumn 69, Issue SUPPL. 8, 2007, Pages 98-107

  Terashi, Genki ^a   Takeda Shitaka, Mayuko ^a   Kanou, Kazuhiko ^a   Iwadate, Mitsuo ^a   Takaya, Daisuke ^a   Hosoi, Akio ^a   Ohta, Kazuhiro ^a   Umeyama, Hideaki ^a  

^a KITASATO UNIVERSITY   (Japan)

Author keywords

CASP; CHIMERA; Comparative modeling; FAMS; Homology modeling; Protein structure prediction; Quality assessment; SKE CHIMERA; TBM template based modeling

Indexed keywords

CONFERENCE PAPER; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN MODIFICATION; PROTEIN QUALITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 36749027045     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21785     Document Type: Conference Paper

References (26)

1. Takeda-Shitaka M, Terashi G, Takaya D, Kanou K, Iwadate M, Umeyama H. Protein structure prediction in CASP6 using CHIMERA and FAMS. Proteins 2005;61(Suppl 7):122-127.
2. Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
3. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
4. Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 2001;313:417-430.
5. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992;356:83-85.
6. Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997;277:396-404.
7. Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomp 2000;5:119-130.
8. Kelley LA, MacCallum RM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:499-520.
9. Wallner B, Elofsson A. Can correct protein models be identified? Protein Sci 2003;12:1073-1086.
10. http://www.cs.bgu.ac.il/~dfischer/CAFASP4/.
11. http://www.cs.bgu.ac.il/~dfischer/CAFASP4/mqap.html.
12. Fischer D. Servers for protein structure prediction. Curr Opin Struct Biol 2006;16:178-182.
13. Tosatto SC. The Victor/FRST function for model quality estimation. J Comput Biol 2005;12:1316-1327.
14. Pettitt CS, McGuffin LJ, Jones DT. Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 2005;21:3509-3515.
15. Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
16. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
17. http://predictioncenter.org/casp7/.
18. Ogata K, Umeyama H. An automatic homology modeling method consisting of database searches and simulated annealing. J Mol Graph Model 2000;18:258-272, 305-256.
19. Anguita D, Boni A, Ridella S, Rivieccio F, Sterpi D. Theoretical and practical model selection methods for support vector classifiers. In: Wang L, editor. Support vector machines: theory and applications, Vol. 177; Berlin: Springer-Verlag; 2005. pp 159-179.
20. Park KJ, Gromiha MM, Horton P, Suwa M. Discrimination of outer membrane proteins using support vector machines. Bioinformatics 2005;21:4223-4229.
21. Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
22. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
23. Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
24. Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;37(Suppl 3):22-29.
25. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
26. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins 1992;12:345-364.