TOUCHSTONE: A Unified Approach to Protein Structure Prediction

Proteins: Structure, Function and Genetics

Volumn 53, Issue SUPPL. 6, 2003, Pages 469-479

  Skolnick, Jeffrey ^a   Zhang, Yang ^a   Arakaki, Adrian K ^a   Kolinski, Andrzej ^a,b   Boniecki, Michal ^b   Szilágyi, András ^a   Kihara, Daisuke ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Ab initio prediction; Comparative modeling; Fold recognition

Indexed keywords

AB INITIO CALCULATION; ALGORITHM; CASP5 TARGET; COMPARATIVE MODEL; CONFERENCE PAPER; DNA TEMPLATE; FOLD RECOGNITION; GENERALIZED COMPARATIVE MODELING; MODEL; PRIORITY JOURNAL; PROSPECTOR ALGORITHM; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; TOUCHSTONE STRUCTURE PREDICTION;

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

EID: 0242299185     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10551     Document Type: Conference Paper

References (28)

1. Rost B, Sander C. Bridging the protein sequence-structure gap by structure predictions. Annu Rev Biophys Biomol Struct 1996;25: 113-136.
2. Finkelstein AV, Reva BA. A search for the most stable folds of protein chains. Nature 1991; 351: 497-499.
3. Fischer D, Elofsson A, Rice D, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac Symp Biocomput 1996; 300-318.
4. Rice DW, 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.
5. Fischer D. Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions. Proteins 1999; Suppl: 61-65.
6. Godzik A, Skolnick J. Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination. Proc. Natl. Acad. Sci. USA 1992; 89: 12098-12102.
7. Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999; 287: 797-815.
8. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001; 42: 319-331.
9. Russell RB, Saqi MAS, Sayle RA, Bates PA, Sternberg MJE. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 1997; 269: 423-439.
10. Levitt M, Gerstein M, Huang E, Subbiah S, Tsai J. Protein folding: the endgame. Annu Rev Biochem 1997; 66: 549-579.
11. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998; 281: 565-577.
12. Ortiz AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins 1999; 37: 177-185.
13. Sternberg MJ, Bates PA, Kelley LA, MacCallum RM. Progress in protein structure prediction: assessment of CASP3. Curr Opin Struct Biol 1999; 9: 368-373.
14. Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci U S A 2001; 98: 10125-10130.
15. McGuffin LJ, Bryson K, Jones DT, The PSIPRED protein structure prediction server. Bioinformatics 2000; 16: 404-405.
16. Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001; 44: 133-149.
17. Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990; 183: 63-98.
18. Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002; 48: 192-201.
19. Swendsen RH, Wang JS. Replica Monte Carlo simulation of spin glasses. Physical Review Letters 1986; 57: 2607-2609.
20. Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 1997; 281: 140-150.
21. Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys J 2003; 85: 1145-1164.
22. Betancourt MR, Skolnick J. Universal similarity measure for comparing protein structures. Biopolymers 2001; 59: 305-309.
23. Zemla A, Venclovas, Moult J, Fidelis K. Processing and evaluation of predictions in CASP4. Proteins 2001; Suppl 5: 13-21.
24. Skolnick J, Kolinski A, Kihara D, Betancourt M, Rotkiewicz P, Boniecki M. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins 2001; Suppl 5: 149-156.
25. 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.
26. Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001; 44: 223-232.
27. Felts AK, Gallicchio E, Wallqvist A, Levy RM. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model, Proteins 2002; 48: 404-422.
28. 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.