Computational Protein Design as a Cost Function Network Optimization Problem, Proceedings of the 18th International Conference on Principles and Practice of Constraint Programming, pp.840-849, 2012. ,
DOI : 10.1007/978-3-642-33558-7_60
URL : https://hal.archives-ouvertes.fr/hal-01191320
An optimal coarse-grained arc consistency algorithm, Artificial Intelligence, vol.165, issue.2, pp.165-185, 2005. ,
DOI : 10.1016/j.artint.2005.02.004
A protein-dependent side-chain rotamer library, BMC Bioinformatics, vol.12, issue.Suppl 14, p.10, 2011. ,
DOI : 10.1109/TIT.2005.850085
Arc consistency for soft constraints, Artificial Intelligence, vol.154, issue.1-2, pp.199-227, 2004. ,
DOI : 10.1016/j.artint.2003.09.002
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
Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding, 1999. ,
Protein Design Using Continuous Rotamers, PLoS Computational Biology, vol.285, issue.1, p.2012 ,
DOI : 10.1371/journal.pcbi.1002335.s002
URL : http://doi.org/10.1371/journal.pcbi.1002335
osprey, Methods in enzymology, vol.523, p.87, 2013. ,
DOI : 10.1016/B978-0-12-394292-0.00005-9
Reactive Answer Set Programming, Proceedings of the Eleventh International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR'11), pp.54-66, 2011. ,
DOI : 10.1007/978-3-642-20895-9_7
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.228.3006
Engineering an Incremental ASP Solver, Proceedings of the Twenty-fourth International Conference on Logic Programming, pp.190-205, 2008. ,
DOI : 10.1016/j.artint.2004.04.004
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.147.9074
On the Implementation of Weight Constraint Rules in Conflict-Driven ASP Solvers, Logic Programming, pp.250-264, 2009. ,
DOI : 10.1007/978-3-540-24605-3_37
Clingo= asp+ control: Preliminary report. arXiv preprint, 2014. ,
The stable model semantics for logic programming, pp.1070-1080, 1988. ,
Classical negation in logic programs and disjunctive databases, New Generation Computing, vol.38, issue.No. 3, pp.365-386, 1991. ,
DOI : 10.1007/BF03037169
URL : http://ai.ustc.edu.cn/cn/seminar/files/Classic_Negation_in_Logic_Programming_and_Disjunctive_Database.pdf
Dead-End Elimination with Backbone Flexibility, ISMB/ECCB (Supplement of Bioinformatics), pp.185-194, 2007. ,
DOI : 10.1093/bioinformatics/btm197
Energy functions for protein design, Current Opinion in Structural Biology, vol.9, issue.4, pp.509-513, 1999. ,
DOI : 10.1016/S0959-440X(99)80072-4
Protein design using answer set programming, Master Dissertation Instituto superior tecnico Lisboa, 2012. ,
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.3671727-1747, 1894. ,
DOI : 10.1038/35102009
Dead-end elimination with perturbations (deeper): A provable protein design algorithm with continuous sidechain and backbone flexibility, Proteins: Structure, Function, and Bioinformatics, vol.81, issue.1, pp.18-39, 2013. ,
A gradient-directed Monte Carlo approach for protein design, Journal of Computational Chemistry, vol.6, issue.11, pp.312164-2168, 2010. ,
DOI : 10.1002/jcc.21506
De Novo Computational Design of Retro-Aldol Enzymes, Science, vol.319, issue.5868, pp.3191387-1391, 2008. ,
DOI : 10.1126/science.1152692
De novo protein design using pairwise potentials and a genetic algorithm, Protein Science, vol.3, issue.4, pp.567-574, 1994. ,
Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction, Journal of Molecular Biology, vol.230, issue.2, pp.543-574, 1993. ,
DOI : 10.1006/jmbi.1993.1170
Protein Modeling Suite Can Do for You, Biochemistry, vol.49, issue.14, pp.2987-2998, 2010. ,
DOI : 10.1021/bi902153g
Improved prediction of protein side-chain conformations with scwrl4, Proteins: Structure, Function, and Bioinformatics, vol.77, issue.4, pp.778-795, 2009. ,
Solving weighted CSP by maintaining arc consistency, Artificial Intelligence, vol.159, issue.1-2, pp.1-26, 2004. ,
DOI : 10.1016/j.artint.2004.05.004
URL : http://doi.org/10.1016/j.artint.2004.05.004
Exploring the conformational space of protein side chains using dead-end elimination and the a* algorithm, Proteins Structure Function and Genetics, vol.33, issue.2, pp.227-239, 1998. ,
Chapter nineteen -rosetta3: An object-oriented software suite for the simulation and design of macromolecules, Methods in Enzymology, vol.487, pp.545-574, 2011. ,
What is answer set programming?, pp.1594-1597, 2008. ,
Engineering a mevalonate pathway in escherichia coli for production of terpenoids, Nature biotechnology, vol.21, issue.7, pp.796-802, 2003. ,
Answer set programming: A declarative approach to solving search problems, Logics in Artificial Intelligence, pp.15-18, 2006. ,
Sat-based protein design, ICCAD, pp.128-135, 2009. ,
Protein engineers turned evolutionists, Nature methods, vol.4, issue.12, pp.991-994, 2007. ,
Protein design is np-hard, Protein Engineering, vol.15, issue.10, pp.779-782, 2002. ,
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
Arc consistency for soft constraints. Principles and Practice of Constraint Programming CP, pp.411-425, 2000. ,
Using genetic algorithm to design protein sequence, Applied Mathematics and Computation, vol.200, issue.1, pp.1-9, 2008. ,
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure, vol.19, issue.6, pp.844-858, 2011. ,
A new framework for computational protein design through cost function network optimization, Bioinformatics, vol.29, issue.17, pp.292129-2136, 2013. ,
DOI : 10.1093/bioinformatics/btt374
Mixed-Integer Linear Programming Algorithm for a Computational Protein Design Problem, Industrial & Engineering Chemistry Research, vol.46, issue.3, pp.839-845, 2007. ,
DOI : 10.1021/ie0605985