SAM-T04: What is new in protein-structure prediction for CASP6

Proteins: Structure, Function and Genetics

Volumn 61, Issue SUPPL. 7, 2005, Pages 135-142

  Karplus, Kevin ^a   Katzman, Sol ^a   Shackleford, George ^a   Koeva, Martina ^a   Draper, Jenny ^a   Barnes, Bret ^a   Soriano, Marcia ^a   Hughey, Richard ^a  

^a University of California Santa Cruz   (United States)

Author keywords

Fold recognition new fold; FRAGFINDER protein fragment finder; Hidden Markov models; Local structure prediction; SAM T04; UNDERTAKER protein conformation generation

Indexed keywords

CONFERENCE PAPER; CRITICAL ASSESSMENT OF PROTEIN STRUCTURE PREDICTION METHOD; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

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

EID: 30344452280     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20730     Document Type: Conference Paper

References (18)

1. Karplus K, Sjölander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. Predicting protein structure using hidden Markov models. Proteins 1997; Suppl 1:134-139.
2. Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R. Predicting protein structure using only sequence information. Proteins 1999; Suppl 3:121-125.
3. 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.
4. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
5. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 2001;17:1242-1243.
6. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 2003;53(Suppl 6):491-496.
7. NR (All Non-Redundant GenBank CDS Translations + PDB + SwissProt + PIR + PRF Database. Distributed on the Internet via anonymous FTP from ftp://ftp.ncbi.nlm.nih.gov/blast/db. Information on NR is available at http://www.ncbi.nlm.nih.gov/BLAST/ blast_databases.html.
8. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. J Mol Biol 1990;215:403-410.
9. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
10. Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin E, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001;29:2994-3005.
11. Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 2003;51:504-514.
12. Karchin R, Cline M, Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins 2004;55:508-518.
13. Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999;Suppl3:171-176.
14. Bower M, Cohen F, Dunbrack R. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
15. Canutescu AA, Shelenkov AA, Dunbrack RL Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
16. Cid H, Bunster M, Canales M, Gazitua F. Hydrophobicity and structural classes in proteins. Protein Eng 1992;5:373-375.
17. Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2000;301:173-190.
18. Zhang Y, Skolnick J. Scoring function for the automated assessment of protein structure template quality. Proteins 2004;57:702-710.