Paircoil2: Improved prediction of coiled coils from sequence

Bioinformatics

Volumn 22, Issue 3, 2006, Pages 356-358

  McDonnell, A V ^a   Jiang, T ^b,c   Keating, A E ^a   Berger, Bab ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c INSTITUTE OF BIOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DNA HELIX; GENE SEQUENCE; INTERMETHOD COMPARISON; METHODOLOGY; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; STRUCTURAL GENOMICS; VALIDATION PROCESS;

EID: 32144456009     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti797     Document Type: Article

References (21)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Berger,B. et al. (1995) Predicting coiled coils by use of pairwise residue correlations. Proc. Natl Acad. Sci. USA, 92, 8259-8263.
3. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
4. Chan,D.C. et al. (1997) Core structure of gp41 from the HIV envelope glycoprotein. Cell, 89, 263-273.
5. Delorenzi,M. and Speed,T. (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 18, 617-625.
6. Fassler,J.H. et al. (2002) B-ZIP proteins encoded by the Drosophila genome: Evaluation of potential dimerizarion partners. Genome Res., 12, 1190-1200.
7. Fong,J.H. et al. (2004) Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol., 5, R11.
8. Gee,M.A. et al. (1997) An extended microtubule-binding structure within the dynein motor domain. Nature, 390, 636-639.
9. Henrick,K. and Thornton,J.M. (1998) PQS: A protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
10. Hobohm,U. and Sander,C. (1994) Enlarged representative set of protein structures. Protein Sci., 3, 522-524.
11. Li,W. et al. (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics, 18, 77-82.
12. Lupas,A. et al. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
13. Morii,H. et al. (1997) Identification of kinesin neck region as a stable alphahelical coiled coil and its thermodynamic characterization. Biochemistry, 36, 1933-1942.
14. Newman,J.R. and Keating,A.E. (2003) Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science, 300, 2097-2101.
15. Singh,M. et al. (1999) LeamCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins. J. Mol. Biol., 290, 1031-1041.
16. Strelkov,S.V. et al. (2003) Molecular architecture of intermediate filaments. BioEssays, 25, 243-251.
17. Thormählen,M. et al. (1998) The coiled-coil helix in the neck of kinesin, J. Struct. Biol., 122, 300-41.
18. Vincentz,M. et al. (2001) Phylogenetic relationships between Arabidopsis and sugarcane bZIP transcriptional regulatory factors. Genet. Mol. Biol., 24, 55-60.
19. Walshaw,J. and Woolfson,D.N. (2001) Socket: A program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol., 307, 1427-1450.
20. Wolf,E. et al. (1997) MultiCoil: A program for predicting two- and three-stranded coiled coils. Protein Sci., 6, 1179-1189.
21. Yonekura,K. et al. (2003) Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature, 424, 643-650.