Automated Prediction of CASP-5 Structures Using the Robetta Server

Proteins: Structure, Function and Genetics

Volumn 53, Issue SUPPL. 6, 2003, Pages 524-533

  Chivian, Dylan ^a   Kim, David E ^a   Malmström, Lars ^a   Bradley, Philip ^a   Robertson, Timothy ^a   Murphy, Paul ^a   Strauss, Charles E M ^b   Bonneau, Richard ^c   Rohl, Carol A ^d   Baker, David ^a,e  

^a UNIVERSITY OF WASHINGTON   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

ab initio modeling; Automated protein structure prediction server; CAFASP; CASP; Comparative modeling; de novo modeling; Domain parsing; Fragment assembly; Fragment insertion; Homology modeling; Rosetta; Sequence alignment; Template based modeling

Indexed keywords

AUTOMATION; CAFASP 3 TARGET; CASP5 TARGET; CLINICAL PROTOCOL; CONFERENCE PAPER; DNA TEMPLATE; MODEL; PCONS 2 STRUCTURE ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; PROTEIN TARGETING; PSI BLAST STRUCTURE ANALYSIS; ROBETTA SERVER; ROSETTA FRAGMENT INSERTION METHOD; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

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

INSERTION SEQUENCES;

EID: 10744230917     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10529     Document Type: Conference Paper

References (29)

1. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
2. Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
3. 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;Suppl 5:119-126.
4. 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.
5. 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.
6. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 2003.
7. Dunbrack RL, Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
8. Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97: 10383-10388.
9. Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;Suppl 3:22-29.
10. Sippl MJ, Lackner P, Domingues FS, Prlic A, Malik R, Andreeva A, Wiederstein M. Assessment of the CASP4 fold recognition category. Proteins 2001;Suppl 5:55-67.
11. 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;Suppl 5:171-183.
12. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
13. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2002;30:276-280.
14. Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14: 755-763.
15. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
16. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
17. 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.
18. Holm L, Sander C. Mapping the protein universe. Science 1996;273: 595-603.
19. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
20. Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322:65-78.
21. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, 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.
22. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
23. Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. Structure prediction meta server. Bioinformatics 2001;17:750-751.
24. Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287: 797-815.
25. 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.
26. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
27. 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;Suppl 5:86-91.
28. Kelley LA, MacCallum RM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:499-520.
29. Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000;119-130.