H. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The Protein Data Bank, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.6, pp.235-242, 2000.
DOI : 10.1107/S0907444902003451

R. A. Laskovski, E. G. Hutchinson, A. D. Michie, A. C. Wallace, M. L. Jones et al., PDBsum: a web-based database of summaries and analyses of all PDB structures, Trends in Biochemical Sciences, vol.22, issue.12, pp.488-490, 1997.
DOI : 10.1016/S0968-0004(97)01140-7

C. W. Hogue, Cn3D: a new generation of three-dimensional molecular structure viewer, Trends in Biochemical Sciences, vol.22, issue.8, pp.314-316, 1997.
DOI : 10.1016/S0968-0004(97)01093-1

G. Neshich, R. C. Togawa, and B. Honig, Sequence To and withIN graphics PDB Viewer (STING-PDB viewer), PDB Quart. News, vol.6, 1998.

C. Sander and R. Schneider, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins: Structure, Function, and Genetics, vol.4, issue.1, pp.56-68, 1991.
DOI : 10.1002/prot.340090107

R. Schneider, A. De-daruvar, and C. Sander, The HSSP database of protein structure-sequence alignments, Nucleic Acids Research, vol.25, issue.1, pp.226-230, 1997.
DOI : 10.1093/nar/25.1.226

R. Schneider and C. Sander, The HSSP database of protein structure-sequence alignments, Nucleic Acids Research, vol.24, issue.1, pp.201-205, 1996.
DOI : 10.1093/nar/24.1.201

P. Bucher and A. Bairoch, A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation, ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. AAAIPress, Menlo Park, pp.53-61, 1994.

A. Nicholls, K. Sharp, and B. Honig, Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins: Structure, Function, and Genetics, vol.39, issue.4, pp.281-296, 1991.
DOI : 10.1002/prot.340110407

O. V. Tsodikov, M. T. Record, . Jr, and Y. V. Sergeev, Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature, Journal of Computational Chemistry, vol.14, issue.6, pp.600-609, 2002.
DOI : 10.1002/jcc.10061

S. Sridharan, A. Nicholls, and B. Honig, A new vertex algorithm to calculate solvent accessible surface areas, Biophys. J, pp.61-174, 1992.

W. Kabsch and C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983.
DOI : 10.1002/bip.360221211

D. Frishman and P. Argos, Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-679, 1995.
DOI : 10.1002/prot.340230412

A. Radzicka and R. Wolfenden, Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution, Biochemistry, vol.27, issue.5, pp.1664-1670, 1988.
DOI : 10.1021/bi00405a042

A. Gattiker, E. Gasteiger, and A. Bairoch, ScanProsite: a reference implementation of a PROSITE scanning tool, Appl. Bioinf, vol.1, pp.107-108, 2002.

D. Gourley and B. Totty, HTTP: The Definitive Guide. O'Reilly and Associates, 2002.

D. Flanagan, Java Script: The Definitive Guide. O'Reilly and Associates, 1998.

M. Campione and K. Walrath, The Java Tutorial?Object Oriented Programming for the Internet, 1996.

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543
URL : https://hal.archives-ouvertes.fr/hal-00435028

R. D. Page, TREEVIEW: An application to display phylogenetic trees on personal computers, Comput. Appl. Biosci, vol.12, pp.357-358, 1996.

I. Shindyalov and P. Bourne, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering Design and Selection, vol.11, issue.9, pp.739-747, 1998.
DOI : 10.1093/protein/11.9.739

A. Yang and B. Honig, Sequence to structure alignment in comparative modeling using PrISM, Proteins: Structure, Function, and Genetics, vol.17, issue.S3, pp.66-72, 1999.
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<66::AID-PROT10>3.0.CO;2-K

G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, Stereochemistry of polypeptide chain configurations, Journal of Molecular Biology, vol.7, issue.1, pp.95-99, 1963.
DOI : 10.1016/S0022-2836(63)80023-6

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

C. A. Caldas, V. P. Coelho, D. Rigden, G. Neshich, A. M. Moro et al., Design and synthesis of germline-based hemi-humanized single-chain Fv against the CD18 surface antigen, Protein Engineering Design and Selection, vol.13, issue.5, pp.353-360, 2000.
DOI : 10.1093/protein/13.5.353

D. Silva, M. C. Grossi-de-sá, M. F. Chrispeels, M. J. Togawa, R. C. Neshich et al., Analysis of structural and physico-chemical parameters involved in the specificity of binding between ??-amylases and their inhibitors, Protein Engineering Design and Selection, vol.13, issue.3, pp.167-177, 2000.
DOI : 10.1093/protein/13.3.167