Dali server: Conservation mapping in 3D

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Holm, Liisa ^a,b   Rosenström, Päivi ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE MAPPING; GENETIC CONSERVATION; GENETIC DATABASE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; WEB BROWSER; CHEMISTRY; INTERNET; PROTEIN DATABASE; STRUCTURAL HOMOLOGY;

BACTERIAL PROTEINS; DATABASES, PROTEIN; INTERNET; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

BACTERIAL PROTEIN;

EID: 77954288774     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq366     Document Type: Article

References (18)

1. Hasegawa,H. and Holm,L. (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol., 19, 381-389.
2. Holm,L., Kääriäinen,S., Rosenstrom,P. and Schenkel,A. (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics, 24, 2780-2781.
3. Veeramalai,M., Ye,Y.Z. and Godzik,A. (2008) TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ string model. BMC Bioinformatics, 9, Art. No. 358.
4. Kawabata,T. and Nishikawa,K. (2000) Protein tertiary structure comparison using the Markov transition model of evolution. Proteins, 41, 108-122.
5. Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst., D60, 2256-2268.
6. Gibrat,J.-F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
7. Leslin,C.M., Abyzov,A. and Ilyin,V.A. (2007) TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Res., 35, D317-D321.
8. Holm,L. and Sander,C. (1995) Dali: a network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
9. Lichtarge,O. and Sowa,M.E. (2002) Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol., 12, 21-27.
10. Landau,M., Mayrose,I., Rosenberg,Y., Glaser,F., Martz,E., Pupko,T. and Ben-Tal,N. (2005) ConSurf: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res., 33, W299-W302.
11. Laskowski,R.A., Watson,J.D. and Thornton,J.M. (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93.
12. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science, 273, 595-603.
13. Andreeva,A., Howorth,D., Chandonia,J.-M., Brenner,S.E., Hubbard,T.J.P., Chothia,C. and Murzin,A.G. (2007) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
14. Sam,V., Tai,C.H., Garnier,J., Gibrat,J.F., Lee,B. and Munson,P.J. (2006) ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. BMC Bioinformatics, 7, 206.
15. Lindahl,E. and Elofsson,A. (2000) Identification of related proteins on family, superfamily and fold level. J. Mol. Biol., 295, 613-625.
16. Rosado,C.J., Buckle,A.M., Law,R.H., Butcher,R.E., Kan,W.T., Bird,C.H., Ung,K., Browne,K.A., Baran,K., Bashtannyk-Puhalovich,T.A. et al. (2007) A common fold mediates vertebrate defense and bacterial attack. Science, 317, 1548-1551.
17. Hadders,M.A., Beringer,D.X. and Gros,P. (2007) Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense. Science, 317, 1552-1554.
18. Lukoyanova,N. and Saibil,H.R. (2008) Friend or foe: the same fold for attack and defense. Trends Immunol., 29, 51-53.