MMM: A sequence-to-structure alignment protocol

Bioinformatics

Volumn 22, Issue 21, 2006, Pages 2691-2692

  Rai, Brajesh K ^a   Madrid Aliste, Carlos J ^a   Fajardo, J Eduardo ^a   Fiser, András ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; WEB BROWSER;

EID: 33750414092     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl449     Document Type: Article

References (17)

1. Boeckmann,B. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365.
2. Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
3. Fiser,A. (2004) Protein structure modeling in the proteomics era. Exp. Rev. Proteom., 1, 97-110.
4. Kosinski,J. et al. (2005) FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6. Proteins, 61 (Suppl. 7), 106-113.
5. Lambert,C. et al. (2002) ESyPred3D: Prediction of proteins 3D structures. Bioinformatics, 18, 1250-1256.
6. Li,W. et al. (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics, 18, 77-82.
7. Madhusudhan,M.S. et al. (2006) Variable gap penalty for protein sequence-structure alignment. Protein Eng. Des. Sel., 19, 129-133.
8. Miyazawa,S. and Jernigan,R.L. (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol., 256, 623.
9. Notredame,C. et al. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205.
10. Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63.
11. Prasad,J.C. et al. (2003) Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics, 19, 1682.
12. Rai,B.K. and Fiser,A. (2006) Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling. Proteins, 63, 644-661.
13. Rice,D.W. and Eisenberg,D. (1997) A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol., 267, 1026.
14. Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins, 14, 309.
15. Sali,A. and Blundell,T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
16. Shi,J. et al. (2001) FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243.
17. Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673.