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. PhD Thesis, University of 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. (program)
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. (program)
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. (program)
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. (the THREADER program is available on the Silicon Graphics at the "Salle des Utilisateurs" of the Service d'Informatique Scientifique of the 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. (program)
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. (program)
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. (the MODELLER program is available on the Silicon Graphics at the "Salle des Utilisateurs" of the Service d'Informatique Scientifique of the 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.
