Bibliographie sommaire

Observation (datant du 16/09) : Cette bibliographie n'est pas complète. A. Lesk doit en particulier m'envoyer une sélection à lui de références à ses travaux. Tous les participants sont cordialement invités à y ajouter d'autres références s'ils le souhaitent (ou des pointeurs sur des programmes ou pages web). Il suffit de me les envoyer à l'adresse : sagot@pasteur.fr. Merci d'avance.

Delarue M., Koehl P. (1995) Statistics on polar and non polar environments in proteins: application to the detection of wrong structures and relationship with the Eisenberg and McLachlan formalism. J. Mol. Biol. 249:675-690.

Derreumaux P. (1997) Folding a 20 amino acid alphabeta peptide with the diffusion process-controlled Monte Carlo method. J. Chem. Phys. 107:1941-1947.

Derreumaux P. (1998) Finding the low-energy forms of avian pancreatic polypeptide with the diffusion process-controlled Monte Carlo method. J. Chem. Phys. 109:1567-1574.

Escalier V., Pothier J., Soldano H. and Viari A. (1998) Pairwise and multiple identification of three dimensional common substructures in proteins. J. Comp. Biol. 5:41-56.

Escalier V. (1997) Algorithmes pour la comparaison de structures moléculaires tridimensionnelles. Thèse de doctorat, Université de Paris VII.

Frishman D. and Argos P. (1996) Incorporation of non-local interactions in protein secondary structure prediction from the amino-acid sequence. Protein Eng. 9:133-142. (programme)

Frishman D. and Argos P. (1997) Seventy-five percent accuracy in portein secondary structure prediction. Proteins: struct., funct., and genetics 27:329-335.

Garnier J., Gibrat J.-F. and Robson B. (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol. 266:540-553.

Gibrat J.-F., Madej T. and Bryant S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6:377-385.

Guex N. and Peitsch M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723. (programme)

Jean P., Pothier J., Dansette P., Mansuy D. and Viari A. (1997) Automated multiple analysis of protein structures: application to homology modeling of cytochromes P450. Proteins: struct., funct., and genetics 28:388-404.

Jones D.T., Miller R.T. and Thornton J.M. (1995) Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins: struct., funct., and genetics 23:387-397.

Jones D.T. and Thornton J.M. (1996) Potential energy functions for threading. Curr. Opin. Struct. Biol. 6:210-216.

Jung B., Lenhof H.-P., Müller P. and Rüb C. (1997) Parallel MD-simulations of synthetic polymers. In Proc. of the 8th SIAM Conference on Parallel Processing for Scientific Computing, CD-ROM.

King R.D. and Sternberg M.J.E. (1996) Identification and application of the concepts important for accurate and reliable protein secondary structure prediction. Protein Sci. 5:2298-2310. (programme)

Koehl P. and Delarue M. (1994) On the use of self-consistent mean field theory to predict protein side-chain conformations and estimate entropies. J. Mol. Biol. 239:249-275.

Koehl P. and Delarue M. (1994) Polar and non polar environment in proteins: implications for binding and folding. Proteins: struct., funct., and genetics 20:264-278.

Koehl P. and Delarue M. (1995) A new self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat. Struct. Biol. 2:163-170.

Koehl P. and Delarue M. (1996) Mean-field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol. 6:222-226.

Lenhof H.-P. (1995) An algorithm for the protein docking problem. In Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism, p 125-139, Schomburg D. and Lessel U. eds.

Lenhof H.-P. (1997) An Algorithm for the Protein Docking Problem. In Proc. of the First Annual International Conference on Computational Molecular Biology RECOMB 97, p 182-191, S. Istrail, P. Pevzner and M.S. Waterman eds. ACM Press.

Lenhof H.-P. (1997) Parallel Protein Puzzle: A new suite of protein docking tools. In Forschung und wissenschaftliches Rechnen: Beitraege zum Heinz-Billing-Preis 1996, p 31-48, Plesser T. and Wittenberg P. eds., GWDG-Bericht Nr. 44.

Madej T., Gibrat J.-F. and Bryant S.H. (1995) Threading a database of protein cores. Proteins: struct., funct., and genetics 23:356-369.

Miller R.T., Jones D.T. and Thornton J.M. (1996) Protein fold recognition by sequence threading: tools and assessment techniques. FASEB J 10:171-178. (programme THREADER installé sur les Silicon Graphics de la salle des utilisateurs du Service d'Informatique Scientifique de l'Institut Pasteur)

Peitsch M.C. (1996) ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24:274-279.

Peitsch M.C., Herzyk P., Wells T.N.C. and Hubbard R.E. (1996) Automated modelling of the transmembrane region of G-protein coupled receptor by SWISS-MODEL. Receptors and Channels 4:161-164.

Peitsch M.C., Wilkins M.R., Tonella L., Sanchez J.-C., Appel R.D. and Hochstrasser D.F. (1997) Large scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: the example of Escherichia coli. Electrophoresis 18:498-501.

Peitsch M.C. (1997) Large scale protein modelling and model repository. in: Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, vol 5, p 234-236, Gaasterland T, Karp P, Karplus K, Ouzounis C, Sander C and Valencia A eds., AAAI Press.

Peitsch M.C. and Guex N. (1997) Large-scale comparative protein modelling. in: Proteome Research: New Frontiers in Functional Genomics, p 177-186, Wilkins M.R., Williams K.L., Appel R.O., Hochstrasser DF eds., Springer.

Poch O. and Delarue O. (1996) Converting sequence block alignments into structural insights. In Methods Enzymol. 266:662-680.

Rost B. and Sander C. (1993) Prediction of secondary structure at better than 70% accuracy. J. Mol. Biol. 232:584-599. (programme)

Rost B. and Sander C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins: struct., funct., and genetics 19:55-72.

Salamov A.A. and Solovyev V.V. (1995) Prediction of protein secondary structure by combining nearest-neighbour algorithms and multiple sequence alignement. J. Mol. Biol. 247:11-15. (programme)

Sali A., Overington J.P., Johnson M.S. and Blundell T.L. (1990) From protein comparison of protein sequences and structures to protein modelling and design. TIBS 15:235-240. (programme MODELLER installé sur les Silicon Graphics de la salle des utilisateurs du Service d'Informatique Scientifique de l'Institut Pasteur)

Sali A. and Blundell T.L. (1990) Definition of a general topological equivalence in protein structures and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212:403-428.

Sali A. and Blundell T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.

Sali A. and Overington J.P. (1994) Derivation of rules for comparative protein modeling from a database of protein structure alignments. J. Mol. Biol. 234:779-815.

Soldano H., Viari A. and Champesme M. (1995) Searching for flexible repeated patterns using a non transitive similarity relation. Pattern Recognition Letters 16:233-246.

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