VII. BASES DE DONNEES-ALGORITHMES-LOGICIELS

BERGER (http://ostrich.lcs.mit.edu/cgi-bin/score)
Berger B., Wilson D.C., Wolf E., Tonchev T., Milla M., and Kim P.S. Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. USA, 92, 8259-8263 (1995).

BLASTP 1.4.9 MP(telnet lovelace.infobiogen.fr, http://www.ncbi.nlm.nih.gov/BLAST)
Altschul S.F., Gish W., Miller W., Myers F.W., and Lipman D.J. Basic local alignment search tools. J. Mol. Biol., 215, 403-410 (1990).

CHARMM
Brooks B., Bruccoleri R., Olafson B., States D., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and molecular dynamics calculations. J. Comp. Chem., 4, 187-217 (1983).

CLUSTALW 1.6
Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acid Res., 22, 4673-4680 (1994).

DPM (http://www.ibcp.fr/serv_pred.html)
Deleage G. and Roux B. An algorithm for protein secondary strcuture prediction based on class prediction.Protein Eng., 1, 289-294 (1987).

FASTA 3.06 (telnet lovelace.infobiogen.fr)
Improved tools for biological sequence comparison. Pearson W.R., and Lipman D.J. Proc. Natl. Acad. Sci. USA, 85, 2444-2448 (1988).

GOR (http://www.ibcp.fr/serv_pred.html)
Gibrat J.F., Garnier J., and Robson B. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol., 198, 425-443 (1987).

IDITIS 3.1 (logiciel édité par Oxford Molecular Ltd, 1997)

LEVIN (http://www.ibcp.fr/serv_pred.html)
Levin J.M. and Garnier J. Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim. Biophys. Acta, 955, 283-295 (1988).

LOS ALAMOS (http://hiv-web.lanl.gov/immuno/)
Base de données sur le VIH.

LUPAS (http://ulrec3.unil.ch/software/COILS_form.html)
Lupas A., Van Dyke M., and Stock J. Predicting coiled coils from proteins sequences. Science, 252, 1162-1164 (1991).

MPSA (Multiple Protein Sequence Analysis)
Logiciel en cours de développement au sein du laboratoire par Christophe Blanchet

ONUSIDA (http://www.unaids.org)
Organisation Mondiale de la Santé (http://www.who.ch/)

PDB 80 (http://www.pdb.bnl.gov/)
Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Jr, Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., and Tasumi. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542 (1977).

PROCHECK
Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of proteins structures. J. Appl. Cryst., 26, 283-291 (1993).

PROSITE 13.0 (http://expasy.hcuge.ch/sprot/prosite.html)
Bairoch A., Bucher P., and Hofmann K. The PROSITE database, its status in 1995. Nucleic Acid Res.24, 189-196 (1996).

RASMOL 2.6
Sayle R.A., Milner-White E.J. RASMOL: biomolecular graphics for all. J. Mol. Biol., 247, 536-540 (1995).

SCOP 1.35 (http://scop.mrc-lmb.cam.ac.uk/scop/)
Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540 (1995).

SOPMA (http://www.ibcp.fr/serv_pred.html)
Geourjon C. and Deleage G. SOPMA: significant imrpovements in protein secondary structure prediction by consensus prediction from multiple alignement. Comput. Appl. Biosci., 11, 681-684 (1995).

SRS (http://www.infobiogen.fr/srs/cgi-bin/srsc)
Etzold T. and Argos P. SRS an indexing and retrieval tool for flat file data libraries. Comput. Appl. Biosci., 9, 49-57 (1993).

SWISSPROT 34.0 (http://expasy.hcuge.ch/sprot/sprot-top.html)
Bairoch A. The SWISS-PROT protein sequence data bank user manual. University of Geneva and EMBL Data Library, European Bioinformatics Institute, Hinxton (Release 34, October 1996).

XPLOR 3.1
Brünger Axel T. XPLOR 3.1: a system for X-ray crystallography and NMR. Yale University Press (1992).