ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3320-3323

  Gouet, Patrice ^b   Robert, Xavier ^b   Courcelle, Emmanuel ^a  

^a Laboratoire de Biologie Moleculaire   (France)

^b INSTITUT DE BIOLOGIE ET CHIMIE DES PROTÉINES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; DNA BINDING PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA BASE; DEVICE; INTERNET; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; METHODOLOGY; PHYSIOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

DATABASES, PROTEIN; DNA-BINDING PROTEINS; INTERNET; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 0043123208     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg556     Document Type: Article

References (21)

1. Chothia,C. and Lesk,A.M. (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globin. J. Mol. Biol., 136, 225-270.
2. Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
3. Gouet,P., Courcelle,E., Stuart,D.I. and Metoz,F. (1999) ESPript: multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308.
4. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
5. Corpet,F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
6. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
7. Frishman,D. and Argos,D. (1995) Knowledge-based secondary structure assignment. Proteins, 23, 566-579.
8. Gouet,P. and Courcelle,E. (2002) ENDscript: a workflow to display sequence and structure information. Bioinformatics, 18, 767-768.
9. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
10. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
11. Brünger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.S., Kuszewski,J., Nilges,M., Pannu,N.S. et al. (2000) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905-921.
12. Esnouf,R.M. (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graphics, 15, 132-134.
13. Kraulis,P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24, 946-950.
14. Servant,F., Bru,C., Carrère,S., Courcelle,E., Gouzy,J., Peyruc,D. and Kahn,D. (2002) ProDom: automated clustering of homologous domains. Brief. Bioinf., 3, 246-251.
15. Rost,B. (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol., 266, 525-539.
16. Combet,C., Blanchet,C., Geourjon,C. and Deléage,G. (2000) NPS" network protein sequence analysis. Trends Biochem. Sci., 25, 147-150.
17. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
18. Henrissat,B. and Bairoch,A. (1996) Updating the sequence-based classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J., 293, 781-788.
19. Robert,X. (2002) PhD thesis, Université Claude Bernard Lyon I.
20. Orengo,C.A., Michie,A.D., Jones,S., Jones,D.T., Swindells,M.B. and Thornton,J.M. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
21. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.