The HHpred interactive server for protein homology detection and structure prediction

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Söding, Johannes ^a   Biegert, Andreas ^a   Lupas, Andrei N ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN SPOVT; UNCLASSIFIED DRUG; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; CALCULATION; CLIENT SERVER APPLICATION; COMPARATIVE STUDY; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; THREE DIMENSIONAL IMAGING; TRANSCRIPTION REGULATION; ACCESS TO INFORMATION; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; INTERMETHOD COMPARISON; SEQUENCE ANALYSIS; SEQUENCE DATABASE; STATISTICAL MODEL; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

BACTERIAL PROTEINS; DATABASES, PROTEIN; INTERNET; MARKOV CHAINS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 23144452044     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki408     Document Type: Article

References (35)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Pearson,W.R. (1991) Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
3. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acid Res., 25, 3389-3402.
4. Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
5. Rychlewski,L., Zhang,B. and Godzik,A. (1998) Fold and function predictions for Mycoplasma genitalium proteins. Fold Des., 3, 229-238.
6. Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
7. Sadreyev,R.I.and Grishin,N.V.(2003)COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
8. vonÖhsen,N., Sommer,I. and Zimmer,R. (2003) Profile-profile alignment: A powerful tool for protein structure prediction. Pac. Symp. Biocomput., 252-263.
9. Panchenko,A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
10. Fischer,D. (2003) 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor. Proteins, 51, 434-441.
11. Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
12. Venclovas,C. and Thelen,M.P. (2000) Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. Nucleic Acids Res., 28, 2481-2493.
13. Zheng,M., Ginalski,K., Rychlewski,L. and Grishin,N. (2005) Protein domain of unknown function DUF1023 is an alpha/beta hydrolase. Proteins, 59, 1-6.
14. Ginalski,K., Rychlewski,L., Baker,D. and Grishin,N.V. (2004) Protein structure prediction for the male-specific region of the human Y chromosome. Proc. Natl Acad. Sci. USA, 101, 2305-2310.
15. Rand,T.A., Ginalski,K., Grishin,N.V. and Wang,X. (2004) Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc. Natl Acad. Sci. USA, 101, 14385-14389.
16. Pawlak,S.D., Radlinska,M., Chmiel,A.A., Bujnicki,J.M. and Skowronek,K.J. (2005) Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: A case study of restriction endonucleases Bsp6I and PVuII. Nucleic Acids Res., 33, 661-671.
17. Kihara,D. and Skolnick,J. (2004) Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins, 55, 464-473.
18. Todd,A.E., Orengo,C.A. and Thornton,J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113-1143.
19. Pawlowski,K., Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Sensitive sequence comparison as protein function predictor. Pac. Symp. Biocomput., 42-53.
20. Kinch,L. and Grishin,N. (2002) Evolution of protein structures and functions. Curr. Opin. Struct. Biol., 12, 400-408.
21. Bourne,P.E., Addess,K.J., Bluhm,W.F., Chen,L., Deshpande,N., Feng,Z., Fleri,W., Green,R., Merino-Ott,J.C., Townsend-Merino,W. et al. (2004) The distribution and query systems of the RCSB protein data bank. Nucleic Acid Res., 32, D223-D225.
22. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
23. Sonnhammer,E.L., Eddy,S.R., Birney,E., Bateman,A. and Durbin,R. (1998) Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.
24. Ponting,C.P., Schultz,J., Milpetz,F. and Bork,P. (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 24, 229-232.
25. Tatusov,R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N. et al. (2003) The COG database: An updated version includes eukaryotes. BMC Bioinformatics, 4, 41-41.
26. Marchler-Bauer,A., Panchenko,A., Shoemaker,B., Thiessen,P., Geer,L. and Bryant,S. (2002) CDD: A database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res., 30, 281-283.
27. Fischer,D., Rychlewski,L., Dunbrack,R.L.J., Ortiz,A.R. and Elofsson,A. (2003) CAFASP3: The third critical assessment of fully automated structure prediction methods. Proteins, 53, 503-516.
28. Söding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
29. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
30. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
31. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
32. Dong,T.C., Cutting,S.M. and Lewis,R.J. (2004) DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT. FEMS Microbiol. Lett., 233, 247-256.
33. O'Reilly,M. and Devine,K.M. (1997) Expression of AbrB, a transition state regulator from Bacillus subtilis, is growth phase dependent in a manner resembling that of Fis, the nucleoid binding protein from Escherichia coli. J. Bacteriol., 179, 522-529.
34. Kamada,K., Hanaoka,F. and Burley,S.K. (2003) Crystal structure of the MazE/MazF complex: Molecular bases of antidote-toxin recognition. Mol. Cell, 11, 875-884.
35. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.