Dramatic performance enhancements for the FASTER optimization algorithm, J. Comput. Chem, vol.27, pp.1071-1075, 2006. ,
Computational protein design as a cost function network optimization problem, Proceedings of Principles and Practice of Constraint Programming-CP 2012, pp.840-849, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01268632
A combinatorial approach to protein docking with flexible side chains, J. Comput. Biol, vol.9, pp.597-612, 2002. ,
A residue-pairwise generalized born scheme suitable for protein design calculations, J. Phys. Chem. B, vol.109, pp.22667-22673, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00770118
Combinatorial and computational challenges for biocatalyst design, Nature, vol.409, pp.253-257, 2001. ,
The Protein Data Bank. A computer-based archival file for macromolecular structures, Eur. J. Biochem, vol.80, pp.319-324, 1977. ,
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations, Proteins, vol.57, pp.400-413, 2004. ,
Radio link frequency assignment, Constraints, vol.4, pp.79-89, 1999. ,
, , vol.9, 2006.
Computational structure-based redesign of enzyme activity, Proc. Natl Acad. Sci. USA, vol.106, pp.3764-3769, 2009. ,
Soft arc consistency revisited, Artif. Intell, vol.174, pp.449-478, 2010. ,
De novo protein design: fully automated sequence selection, Science, vol.278, pp.82-87, 1997. ,
Existential arc consistency: getting closer to full arc consistency in weighted CSPs, Proceedings of 19th International Joint Conference on Artificial Intelligence, pp.84-89, 2005. ,
Mendelsoft: Mendelian error detection in complex pedigree using weighted constraint satisfaction techniques, Proceedings of 8th World Congress on Genetics Applied to Livestock Production, vol.2, 2006. ,
De novo design of the hydrophobic cores of proteins, Protein Sci, vol.4, pp.2006-2018, 1995. ,
The dead-end elimination theorem and its use in protein sidechain positioning, Nature, vol.356, pp.539-542, 1992. ,
Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization, Proteins, vol.48, pp.31-43, 2002. ,
Protein design using continuous rotamers, PLoS Comput. Biol, vol.8, p.1002335, 2012. ,
Dead-end elimination with backbone flexibility, Bioinformatics, vol.23, pp.185-194, 2007. ,
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, J. Comput. Chem, vol.29, pp.1527-1542, 2008. ,
Algorithm for backrub motions in protein design, Bioinfmatics, vol.24, pp.196-204, 2008. ,
Branch-and-terminate: a combinatorial optimization algorithm for protein design, Structure, vol.7, pp.1089-1098, 1999. ,
Mimicking biopolymers on a molecular scale: nano(bio)technology based on engineered proteins, Philos. Trans. A Math. Phys. Eng. Sci, vol.367, pp.1727-1747, 2009. ,
Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility, Proteins, vol.81, pp.18-39, 2013. ,
Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium, J. Phys. Chem, vol.100, pp.19824-19839, 1996. ,
Construction of new ligand binding sites in proteins of known structure: I. Computer-aided modeling of sites with predefined geometry, J. Mol. Biol, vol.222, pp.763-785, 1991. ,
Rotamer optimization for protein design through MAP estimation and problem-size reduction, J. Comput. Chem, vol.30, pp.1923-1945, 2009. ,
Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins, vol.65, pp.712-725, 2006. ,
Prediction of protein-protein interface sequence diversity using flexible backbone computational protein design, Structure, vol.16, pp.1777-1788, 2008. ,
Conformation of amino acid sidechains in proteins, J. Mol. Biol, vol.125, pp.357-386, 1978. ,
Solving and analyzing side-chain positioning problems using linear and integer programming, Bioinformatics, vol.21, pp.1028-1036, 2005. ,
GLYCAM06: a generalizable biomolecular force field. Carbohydrates, J. Comput. Chem, vol.29, pp.622-655, 2008. ,
Solving frequency assignment problems via tree-decomposition, Electron. Notes Discrete Math, vol.3, pp.102-105, 1999. ,
Native protein sequences are close to optimal for their structures, Proc. Natl Acad. Sci. USA, vol.97, pp.10383-10388, 2000. ,
Solving weighted CSP by maintaining arc consistency, Artif. Intell, vol.159, pp.1-26, 2004. ,
Reversible DAC and other improvements for solving Max-CSP, Proceedings of the National Conference on Artificial Intelligence, pp.347-352, 1998. ,
Existential arc consistency: getting closer to full arc consistency in weighted CSPs, Proceedings of the 19th International Joint Conference on Artificial Intelligence, pp.84-89, 2005. ,
Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm, Proteins, vol.33, pp.227-239, 1998. ,
An adaptive dynamic programming algorithm for the side chain placement problem, Pac. Symp. Biocomput, pp.16-27, 2005. ,
Reasoning from last conflict (s) in constraint programming, Artif. Intell, vol.173, pp.1592-1614, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00868108
Computational design of antibody affinity improvement beyond in vitro maturation, Nat. Biotechnol, vol.25, pp.1171-1176, 2007. ,
Recent progress in industrial biocatalysis, Curr. Opin. Chem. Biol, vol.15, pp.187-193, 2011. ,
Molecular technology: designing proteins and peptides, Nature, vol.301, 0200. ,
Protein design is NP-hard, Protein Eng, vol.15, pp.779-782, 2002. ,
Prediction of amino acid sequence from structure, Protein Sci, vol.9, pp.1106-1119, 2000. ,
Arc consistency for soft constraints, Proceedings of Principles and Practice of Constraint Programming-CP, pp.411-425, 2000. ,
Valued constraint satisfaction problems: hard and easy problems, Int. Joint Conf. Artif. Intell, vol.14, pp.631-639, 1995. ,
Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design, J. Mol. Biol, vol.299, pp.789-803, 2000. ,
Enhancements of branch and bound methods for the maximal constraint satisfaction problem, Proceedings of the thirteenth national conference on Artificial Intelligence (AAAI-96), pp.188-195, 1996. ,
Development and testing of a general AMBER force field, J. Comp. Chem, vol.25, pp.1157-1174, 2004. ,
Automatic atom type and bond type perception in molecular mechanical calculations, J. Mol. Graph. Model, vol.25, p.247260, 2006. ,
Automatic protein design with all atom force fields by exact and heuristic optimization, J. Mol. Biol, vol.301, pp.713-736, 2000. ,
DARN! A weighted constraint solver for RNA motif localization, Constraints, vol.13, pp.91-109, 2008. ,