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

G. Neshich, R. Togawa, A. L. Mancini, P. R. Kuser, M. E. Yamagishi et al., STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence, Nucleic Acids Research, vol.31, issue.13, pp.3386-3392, 2003.
DOI : 10.1093/nar/gkg578
URL : https://hal.archives-ouvertes.fr/hal-01092995

G. Neshich, W. Rocchia, A. L. Mancini, M. E. Yamagishi, P. R. Kuser et al., JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure, Nucleic Acids Research, vol.32, issue.Web Server, pp.595-601, 2004.
DOI : 10.1093/nar/gkh480

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

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

R. A. Laskowski, 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

R. H. Higa, A. J. Montagner, R. C. Togawa, P. R. Kuser, M. E. Yamagishi et al., ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure, Bioinformatics, vol.20, issue.12, 1983.
DOI : 10.1093/bioinformatics/bth185

R. H. Higa, A. G. Oliveira, L. G. Horita, R. T. Miura, M. K. Inoue et al., Defining 3D residue environment in protein structures using SCORPION and FORMIGA, Bioinformatics, vol.20, issue.12, 1989.
DOI : 10.1093/bioinformatics/bth190

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

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

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
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.9420

T. Pupko, R. E. Bell, I. Mayrose, F. Glaser, and N. Ben-tal, Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues, Bioinformatics, vol.18, issue.Suppl 1, pp.71-77, 2002.
DOI : 10.1093/bioinformatics/18.suppl_1.S71

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. 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

J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, and S. Subramaniam, Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins, Proteins: Structure, Function, and Genetics, vol.70, issue.1, pp.18-29, 1998.
DOI : 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H

W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera et al., Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects, Journal of Computational Chemistry, vol.16, issue.1, pp.128-137, 2002.
DOI : 10.1002/jcc.1161

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