B. Roux and T. Simonson, Implicit solvent models, Biophysical Chemistry, vol.78, issue.1-2, pp.1-20, 1999.
DOI : 10.1016/S0301-4622(98)00226-9

D. Eisenberg and A. Mcclachlan, Solvation energy in protein folding and binding, Nature, vol.32, issue.6050, pp.199-203, 1986.
DOI : 10.1038/319199a0

L. Wesson and D. Eisenberg, Atomic solvation parameters applied to molecular dynamics of proteins in solution, Protein Science, vol.20, issue.4, pp.227-235, 1992.
DOI : 10.1002/pro.5560010204

F. Fraternali and W. Van-gunsteren, An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution, Journal of Molecular Biology, vol.256, issue.5, pp.939-948, 1996.
DOI : 10.1006/jmbi.1996.0139

P. Ferrara, J. Apostolakis, and A. Caflisch, Evaluation of a fast implicit solvent model for molecular dynamics simulations, Proteins: Structure, Function, and Genetics, vol.26, issue.1, pp.24-33, 2002.
DOI : 10.1002/prot.10001

P. Koehl and M. Delarue, Polar and nonpolar atomic environments in the protein core: Implications for folding and binding, Proteins: Structure, Function, and Genetics, vol.241, issue.3, pp.264-278, 1994.
DOI : 10.1002/prot.340200307

A. Juffer, F. Eisenhaber, S. Hubbard, and D. Walther, Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding, Protein Science, vol.93, issue.12, pp.2499-2509, 1995.
DOI : 10.1002/pro.5560041206

J. Pei, Q. Wang, J. Zhou, and L. Lai, Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation, Proteins: Structure, Function, and Bioinformatics, vol.19, issue.4, pp.661-664, 2004.
DOI : 10.1002/prot.20198

M. Feig, C. Brooks, and . Iii, Recent advances in the development and application of implicit solvent models in biomolecule simulations, Current Opinion in Structural Biology, vol.14, issue.2, pp.217-224, 2004.
DOI : 10.1016/j.sbi.2004.03.009

T. Simonson, Macromolecular electrostatics: continuum models and their growing pains, Current Opinion in Structural Biology, vol.11, issue.2, pp.243-252, 2001.
DOI : 10.1016/S0959-440X(00)00197-4

B. Honig and A. Nicholls, Classical electrostatics in biology and chemistry, Science, vol.268, issue.5214, pp.1144-1149, 1995.
DOI : 10.1126/science.7761829

T. Simonson, Electrostatics and dynamics of proteins, Reports on Progress in Physics, vol.66, issue.5, pp.737-787, 2003.
DOI : 10.1088/0034-4885/66/5/202

URL : https://hal.archives-ouvertes.fr/hal-00770715

G. Archontis and T. Simonson, A Residue-Pairwise Generalized Born Scheme Suitable for Protein Design Calculations, The Journal of Physical Chemistry B, vol.109, issue.47, pp.22667-22673, 2005.
DOI : 10.1021/jp055282+

URL : https://hal.archives-ouvertes.fr/hal-00770118

T. Ooi, M. Oobatake, G. Nemethy, and H. Scheraga, Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides., Proceedings of the National Academy of Sciences, vol.84, issue.10, pp.3086-3090, 1987.
DOI : 10.1073/pnas.84.10.3086

W. Wang, W. Lim, A. Jakalian, J. Wang, R. Luo et al., An Analysis of the Interactions between the Sem???5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis, Journal of the American Chemical Society, vol.123, issue.17, pp.3986-3994, 2001.
DOI : 10.1021/ja003164o

T. Hou, X. Qiao, W. Zhang, and X. Xu, Empirical Aqueous Solvation Models Based on Accessible Surface Areas with Implicit Electrostatics, The Journal of Physical Chemistry B, vol.106, issue.43, pp.11295-11304, 2002.
DOI : 10.1021/jp025595u

A. Lopes, A. Aleksandrov, C. Bathelt, G. Archontis, and T. Simonson, Computational sidechain placement and protein mutagenesis with implicit solvent models, Proteins: Structure, Function, and Bioinformatics, vol.18, issue.4, pp.853-867, 2007.
DOI : 10.1002/prot.21379

D. Bolon and S. Mayo, Enzyme-like proteins by computational design, Proceedings of the National Academy of Sciences, vol.98, issue.25, pp.14274-14279, 2001.
DOI : 10.1073/pnas.251555398

S. Liang and N. Grishin, Effective scoring function for protein sequence design, Proteins: Structure, Function, and Bioinformatics, vol.247, issue.2, pp.271-281, 2004.
DOI : 10.1002/prot.10560

H. Hellinga and F. Richards, Optimal sequence selection in proteins of known structure by simulated evolution., Proceedings of the National Academy of Sciences, vol.91, issue.13, pp.5803-5807, 1994.
DOI : 10.1073/pnas.91.13.5803

L. Wernisch, S. Héry, and S. Wodak, Automatic protein design with all atom force-fields by exact and heuristic optimization, Journal of Molecular Biology, vol.301, issue.3, pp.713-736, 2000.
DOI : 10.1006/jmbi.2000.3984

B. Kuhlman and D. Baker, Native protein sequences are close to optimal for their structures, Proceedings of the National Academy of Sciences, vol.97, issue.19, pp.10383-10388, 2000.
DOI : 10.1073/pnas.97.19.10383

P. Koehl and M. Levitt, Protein topology and stability define the space of allowed sequences, Proceedings of the National Academy of Sciences, vol.99, issue.3, pp.1280-1285, 2002.
DOI : 10.1073/pnas.032405199

G. Dantas, B. Kuhlman, D. Callender, M. Wong, and D. Baker, A Large Scale Test of Computational Protein Design: Folding and Stability of Nine Completely Redesigned Globular Proteins, Journal of Molecular Biology, vol.332, issue.2, pp.449-460, 2003.
DOI : 10.1016/S0022-2836(03)00888-X

C. Saunders and D. Baker, Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design, Journal of Molecular Biology, vol.346, issue.2, pp.631-644, 2005.
DOI : 10.1016/j.jmb.2004.11.062

H. Madaoui, E. Becker, and R. Guérois, Sequence Search Methods and Scoring Functions for the Design of Protein Structures, Methods Mol Biol, vol.340, pp.183-206, 2006.
DOI : 10.1385/1-59745-116-9:183

S. Kang and J. Saven, Computational protein design: structure, function and combinatorial diversity, Current Opinion in Chemical Biology, vol.11, issue.3, pp.329-334, 2007.
DOI : 10.1016/j.cbpa.2007.05.006

H. Zhou and Y. Zhou, Stability scale and atomic solvation parameters extracted from 1023 mutation experiments, Proteins: Structure, Function, and Genetics, vol.11, issue.4, pp.483-492, 2002.
DOI : 10.1002/prot.10241

A. Lomize, M. Reibarkh, and I. Pogozheva, Interatomic potentials and solvation parameters from protein engineering data for buried residues, Protein Science, vol.5, issue.(Suppl.), pp.1984-2000, 2002.
DOI : 10.1110/ps.0307002

G. Makhatadze and P. Privalov, Energetics of interactions of aromatic hydrocarbons with water, Biophysical Chemistry, vol.50, issue.3, pp.285-291, 1994.
DOI : 10.1016/0301-4622(93)E0096-N

S. Rick and B. Berne, Free Energy of the Hydrophobic Interaction from Molecular Dynamics Simulations:?? The Effects of Solute and Solvent Polarizability, The Journal of Physical Chemistry B, vol.101, issue.49, pp.10488-10493, 1997.
DOI : 10.1021/jp971579z

X. Huang, C. Margulis, and B. Berne, Do Molecules as Small as Neopentane Induce a Hydrophobic Response Similar to That of Large Hydrophobic Surfaces?, The Journal of Physical Chemistry B, vol.107, issue.42, pp.11742-11748, 2003.
DOI : 10.1021/jp030652k

C. Gambacorti-passerini, R. Gunby, R. Piazza, A. Galietta, R. Rostagno et al., Molecular mechanisms of resistance to imatinib in Philadelphia-chromosome-positive leukaemias, The Lancet Oncology, vol.4, issue.2, pp.75-85, 2003.
DOI : 10.1016/S1470-2045(03)00979-3

M. Almlöf, J. Aqvist, A. Smalas, and B. Bransdal, Probing the Effect of Point Mutations at Protein-Protein Interfaces with Free Energy Calculations, Biophysical Journal, vol.90, issue.2, pp.433-442, 2006.
DOI : 10.1529/biophysj.105.073239

D. Krowarsch, M. Dadlez, O. Buczek, I. Krokoszynska, A. Smalas et al., Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases, Journal of Molecular Biology, vol.289, issue.1, pp.175-186, 1999.
DOI : 10.1006/jmbi.1999.2757

R. Guérois, J. Nielsen, and L. Serrano, Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations, Journal of Molecular Biology, vol.320, issue.2, pp.369-387, 2002.
DOI : 10.1016/S0022-2836(02)00442-4

N. Pokola and T. Handel, Energy Functions for Protein Design: Adjustment with Protein???Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity, Journal of Molecular Biology, vol.347, issue.1, pp.203-227, 2005.
DOI : 10.1016/j.jmb.2004.12.019

G. Hawkins, C. Cramer, and D. Truhlar, Pairwise solute descreening of solute charges from a dielectric medium, Chemical Physics Letters, vol.246, issue.1-2, pp.122-129, 1995.
DOI : 10.1016/0009-2614(95)01082-K

W. Cornell, P. Cieplak, C. Bayly, I. Gould, K. Merz et al., A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, Journal of the American Chemical Society, vol.117, issue.19, pp.5179-5197, 1995.
DOI : 10.1021/ja00124a002

M. Schaefer and M. Karplus, A Comprehensive Analytical Treatment of Continuum Electrostatics, The Journal of Physical Chemistry, vol.100, issue.5, pp.1578-1599, 1996.
DOI : 10.1021/jp9521621

N. Calimet, M. Schaefer, and T. Simonson, Protein molecular dynamics with the generalized born/ACE solvent model, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.144-158, 2001.
DOI : 10.1002/prot.1134

B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan et al., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Journal of Computational Chemistry, vol.I, issue.2, pp.187-217, 1983.
DOI : 10.1002/jcc.540040211

. Schmidt, M. Busch, A. Lopes, D. Mignon, and T. Simonson, Computational protein design: Software implementation, parameter optimization, and performance of a simple model, Journal of Computational Chemistry, vol.109, issue.7, 2007.
DOI : 10.1002/jcc.20870

URL : https://hal.archives-ouvertes.fr/hal-00488192

T. Simonson, M. D. Schmidt-am-busch, M. Lopes, A. Bathelt, and C. , The inverse protein folding problem: structure prediction in the genomic era, Distributed & Grid Computing ? Science Made Transparent for Everyone. Principles, Applications and Supporting Communities Tektum Publishers, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00772027

A. Jaramillo, L. Wernisch, S. Héry, and S. Wodak, Folding free energy function selects native-like protein sequences in the core but not on the surface, Proceedings of the National Academy of Sciences, vol.99, issue.21, pp.13554-13559, 2002.
DOI : 10.1073/pnas.212068599

S. Larson, A. Garg, J. Desjarlais, and V. Pande, Increased detection of structural templates using alignments of designed sequences, Proteins: Structure, Function, and Genetics, vol.51, issue.3, pp.390-396, 2003.
DOI : 10.1002/prot.10346

B. Lee and F. Richards, The interpretation of protein structures: Estimation of static accessibility, Journal of Molecular Biology, vol.55, issue.3, pp.379-400, 1971.
DOI : 10.1016/0022-2836(71)90324-X

A. Brünger, X-PLOR version 3.1, A System for X-ray crystallography and, 1992.

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000.
DOI : 10.1093/nar/28.1.235

N. Guex and M. Peitsch, SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling, Electrophoresis, vol.23, issue.15, pp.2714-2723, 1997.
DOI : 10.1002/elps.1150181505

P. Tuffery, C. Etchebest, S. Hazout, and R. Lavery, A New Approach to the Rapid Determination of Protein Side Chain Conformations, Journal of Biomolecular Structure and Dynamics, vol.6, issue.6, p.1267, 1991.
DOI : 10.1080/07391102.1986.10506361

URL : https://hal.archives-ouvertes.fr/hal-00313445

M. Kumar, K. Bava, M. Gromiha, P. Parabakaran, K. Kitajima et al., ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions, Nucleic Acids Research, vol.34, issue.90001, pp.204-206, 2006.
DOI : 10.1093/nar/gkj103

S. Park, W. Shalongo, and E. Stellwagen, Residue helix parameters obtained from dichroic analysis of peptides of defined sequence, Biochemistry, vol.32, issue.27, pp.7048-7053, 1993.
DOI : 10.1021/bi00078a033

J. Yang, E. Spek, Y. Gong, H. Zhou, and N. Kallenbach, The role of context on alpha-helix stabilization: host-guest analysis in a mixed background peptide model, Prot Sci, vol.6, issue.6, pp.1-9, 1997.

R. Varadarajan, P. Connelly, J. Sturtevant, and F. Richards, Heat capacity changes for protein-peptide interactions in the ribonuclease S system, Biochemistry, vol.31, issue.5, pp.1421-1426, 1992.
DOI : 10.1021/bi00120a019

S. Padmanabhan, S. Marqusee, T. Ridgeway, T. Laue, and R. Baldwin, Relative helix-forming tendencies of nonpolar amino acids, Nature, vol.344, issue.6263, pp.268-270, 1990.
DOI : 10.1038/344268a0

C. Lyu, M. Liff, L. Marky, and N. Kallenbach, Side chain contributions to the stability of alpha-helical structure in peptides, Science, vol.250, issue.4981, pp.669-673, 1990.
DOI : 10.1126/science.2237416

K. Shoemaker, P. Kim, D. Brems, S. Marqusee, E. York et al., Nature of the charged-group effect on the stability of the C-peptide helix., Proceedings of the National Academy of Sciences, vol.82, issue.8, pp.2349-2353, 1985.
DOI : 10.1073/pnas.82.8.2349

D. Anderson, BOINC: A System for Public-Resource Computing and Storage, Fifth IEEE/ACM International Workshop on Grid Computing, 2004.
DOI : 10.1109/GRID.2004.14

C. Ho and A. Fersht, Internal thermodynamics of position 51 mutants and natural variants of tyrosyl-tRNA synthetase, Biochemistry, vol.25, issue.8, pp.1891-1897, 1986.
DOI : 10.1021/bi00356a009

T. Wells and A. Fersht, Use of binding energy in catalysis analyzed by mutagenesis of the tyrosyl-tRNA synthetase, Biochemistry, vol.25, issue.8, pp.1881-1886, 1986.
DOI : 10.1021/bi00356a007

E. First and A. Fersht, Mutational and kinetic analysis of a mobile loop in tyrosyl-tRNA synthetase, Biochemistry, vol.32, issue.49, pp.13658-13663, 1993.
DOI : 10.1021/bi00212a034

D. Gay, G. Duckworth, H. Fersht, and A. , Modification of the amino acid specificity of tyrosyl-tRNA synthetase by protein engineering, FEBS Letters, vol.318, pp.167-171, 1993.

A. Fersht, R. Leatherbarrow, and T. Wells, Structure-activity relationships in engineered proteins: analysis of use of binding energy by linear free energy relationships, Biochemistry, vol.26, issue.19, pp.6030-6038, 1987.
DOI : 10.1021/bi00393a013

K. Sharp, Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations, Proteins: Structure, Function, and Genetics, vol.90, issue.1, pp.39-48, 1998.
DOI : 10.1002/(SICI)1097-0134(19981001)33:1<39::AID-PROT4>3.0.CO;2-G

U. Moebius, L. Clayton, S. Abraham, S. Harrison, and E. Reinherz, The human immunodeficiency virus gp120 binding site on CD4: delineation by quantitative equilibrium and kinetic binding studies of mutants in conjunction with a high-resolution CD4 atomic structure, Journal of Experimental Medicine, vol.176, issue.2, pp.507-517, 1992.
DOI : 10.1084/jem.176.2.507

J. Cavarelli, G. Eriani, R. B. Ruff, M. Boeglin, M. Mitschler et al., The active site of yeast aspartyltRNA synthetase: structural and functional aspects of the aminoacylation reaction, EMBO J, vol.13, pp.327-337, 1994.