C. Anfinsen, Principles that Govern the Folding of Protein Chains, Science, vol.181, issue.4096, pp.223-253, 1973.
DOI : 10.1126/science.181.4096.223

S. Bistarelli, B. Faltings, and N. Neagu, Interchangeability in soft csps, International Workshop on Constraint Solving and Constraint Logic Programming, pp.31-46, 2002.

F. Boas and P. Harbury, Potential energy functions for protein design, Current Opinion in Structural Biology, vol.17, issue.2, pp.199-204, 2007.
DOI : 10.1016/j.sbi.2007.03.006

M. Cooper, S. De-givry, M. Sanchez, T. Schiex, M. Zytnicki et al., Soft arc consistency revisited, Artificial Intelligence, vol.174, issue.7-8, pp.449-478, 2010.
DOI : 10.1016/j.artint.2010.02.001

URL : http://doi.org/10.1016/j.artint.2010.02.001

M. C. Cooper, S. De-givry, and T. Schiex, Optimal soft arc consistency, Proc. of IJCAI'2007, pp.68-73, 2007.

M. Cooper, Fundamental properties of neighbourhood substitution in constraint satisfaction problems, Artificial Intelligence, vol.90, issue.1-2, pp.1-24, 1997.
DOI : 10.1016/S0004-3702(96)00018-5

B. Dahiyat and S. Mayo, Protein design automation, Protein Science, vol.1, issue.5, pp.895-903, 1996.
DOI : 10.1002/pro.5560050511

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143401

J. Desmet, M. Maeyer, B. Hazes, and I. Lasters, The dead-end elimination theorem and its use in protein side-chain positioning, Nature, vol.356, issue.6369, pp.539-542, 1992.
DOI : 10.1038/356539a0

J. Desmet, J. Spriet, and I. Lasters, Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization, Proteins: Structure, Function, and Genetics, vol.10, issue.1, pp.31-43, 2002.
DOI : 10.1002/prot.10131

A. Fersht, Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding, 1999.

I. Georgiev, R. Lilien, and B. Donald, Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design, Bioinformatics, vol.22, issue.14, pp.174-183, 2006.
DOI : 10.1093/bioinformatics/btl220

I. Georgiev, R. Lilien, and B. Donald, The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles, Journal of Computational Chemistry, vol.23, issue.10, pp.1527-1542, 2008.
DOI : 10.1002/jcc.20909

R. Goldstein, Efficient rotamer elimination applied to protein side-chains and related spin glasses, Biophysical Journal, vol.66, issue.5, pp.1335-1340, 1994.
DOI : 10.1016/S0006-3495(94)80923-3

I. Grunwald, K. Rischka, S. Kast, T. Scheibel, and H. Bargel, Mimicking biopolymers on a molecular scale: nano(bio)technology based on engineered proteins, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.98, issue.6859, pp.1727-1747, 1894.
DOI : 10.1038/35102009

W. D. Harvey and M. L. Ginsberg, Limited discrepency search, Proc. of the 14 th IJCAI, 1995.

G. Hawkins, C. Cramer, and D. Truhlar, Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium, The Journal of Physical Chemistry, vol.100, issue.51, pp.19824-19839, 1996.
DOI : 10.1021/jp961710n

S. Khare, Y. Kipnis, R. Takeuchi, Y. Ashani, M. Goldsmith et al., Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis, Nature Chemical Biology, vol.374, issue.3, pp.294-300, 2012.
DOI : 10.1016/j.cbi.2010.02.039

C. Kingsford, B. Chazelle, and M. Singh, Solving and analyzing side-chain positioning problems using linear and integer programming, Bioinformatics, vol.21, issue.7, pp.1028-1039, 2005.
DOI : 10.1093/bioinformatics/bti144

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.112.9945

A. Koster, S. Van-hoesel, and A. Kolen, Solving Frequency Assignment Problems via Tree-Decomposition, Electronic Notes in Discrete Mathematics, vol.3, 1999.
DOI : 10.1016/S1571-0653(05)00746-8

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, p.10383, 2000.
DOI : 10.1073/pnas.97.19.10383

J. Larrosa, S. De-givry, F. Heras, and M. Zytnicki, Existential arc consistency: getting closer to full arc consistency in weighted CSPs, Proc. of the 19 th IJCAI, pp.84-89, 2005.

J. Larrosa, P. Meseguer, T. Schiex, and G. Verfaillie, Reversible DAC and other improvements for solving max-CSP, Proc. of AAAI'98, 1998.

A. Leach and A. Lemon, Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm, Proteins: Structure, Function, and Genetics, vol.79, issue.2, pp.227-239, 1998.
DOI : 10.1002/(SICI)1097-0134(19981101)33:2<227::AID-PROT7>3.0.CO;2-F

L. Looger and H. Hellinga, Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics, Journal of Molecular Biology, vol.307, issue.1, pp.429-445, 2001.
DOI : 10.1006/jmbi.2000.4424

S. Lovell, J. Word, J. Richardson, and D. Richardson, The penultimate rotamer library, Proteins: Structure, Function, and Genetics, vol.38, issue.3, pp.389-408, 2000.
DOI : 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2

B. Nestl, B. Nebel, and B. Hauer, Recent progress in industrial biocatalysis, Current Opinion in Chemical Biology, vol.15, issue.2, pp.187-193, 2011.
DOI : 10.1016/j.cbpa.2010.11.019

C. Pabo, Molecular technology: Designing proteins and peptides, Nature, vol.281, issue.5897, p.200, 1983.
DOI : 10.1038/301200a0

S. Peisajovich and D. Tawfik, Protein engineers turned evolutionists, Nature Methods, vol.103, issue.12, pp.991-994, 2007.
DOI : 10.1038/nmeth1207-991

N. Pierce, J. Spriet, J. Desmet, and S. Mayo, Conformational splitting: A more powerful criterion for dead-end elimination, Journal of Computational Chemistry, vol.9, issue.11, pp.999-1009, 2000.
DOI : 10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A

N. Pierce and E. Winfree, Protein Design is NP-hard, Protein Engineering Design and Selection, vol.15, issue.10, pp.779-782, 2002.
DOI : 10.1093/protein/15.10.779

J. Pleiss, Protein design in metabolic engineering and synthetic biology, Current Opinion in Biotechnology, vol.22, issue.5, pp.611-617, 2011.
DOI : 10.1016/j.copbio.2011.03.004

K. Raha, A. Wollacott, M. Italia, and J. Desjarlais, Prediction of amino acid sequence from structure, Protein Science, vol.106, issue.8, pp.1106-1119, 2000.
DOI : 10.1110/ps.9.6.1106

T. Schiex, Arc Consistency for Soft Constraints, LNCS, vol.1894, pp.411-424, 2000.
DOI : 10.1007/3-540-45349-0_30

M. Swain and G. Kemp, A CLP Approach to the Protein Side-Chain Placement Problem, Principles and Practice of Constraint Programming?CP, pp.479-493, 2001.
DOI : 10.1007/3-540-45578-7_33

C. Voigt, D. Gordon, and S. Mayo, Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design, Journal of Molecular Biology, vol.299, issue.3, pp.789-803, 2000.
DOI : 10.1006/jmbi.2000.3758

R. Wallace, Directed arc consistency preprocessing, Selected papers from the ECAI-94 Workshop on Constraint Processing, pp.121-137, 1995.
DOI : 10.1007/3-540-59479-5_22