Computational thermostabilization of an enzyme, Science, vol.308, pp.857-860, 2005. ,
Computational design and selections for an engineered, thermostable terpene synthase, Protein Sci, vol.20, pp.1597-1606, 2011. ,
Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo, J. Virol, vol.88, pp.12669-12682, 2014. ,
Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity, PLoS Comput. Biol, vol.8, pp.1-12, 2012. ,
Computer-aided engineering of a transglycosylase for the glucosylation of an unnatural disaccharide of relevance for bacterial antigen synthesis, ACS Catal, vol.5, pp.1186-1198, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02043360
Novel proteins: from fold to function, Curr. Opin. Chem. Biol, vol.15, pp.421-426, 2011. ,
De novo computational design of retro-aldol enzymes, Science, vol.319, pp.1387-1391, 2008. ,
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis, Nat. Chem. Biol, vol.8, pp.294-300, 2012. ,
Design of a novel globular protein fold with atomic-level accuracy, vol.302, pp.1364-1368, 2003. ,
Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility, Proteins: Struct., Funct., Bioinf, vol.81, pp.18-39, 2013. ,
Protein side chain conformation predictions with an MMGBSA energy function, Proteins: Struct., Funct., Bioinf, vol.84, pp.803-819, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01456152
Search-based methods to bound diagnostic probabilities in very large belief nets, Seventh conference on Uncertainty in Artificial Intelligence, pp.142-150, 1991. ,
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 ,
Approximate counting with deterministic guarantees for affinity computation. International Conference on Modelling, Computation and Optimization in Information Systems, Proceedings of the 3rd International Conference on Modelling, Computation and Optimization in Information Systems and Management Sciences, pp.165-176, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01269259
Guaranteed weighted counting for affinity computation: Beyond determinism and structure, International Conference on Principles and Practice of Constraint Programming, pp.733-750, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01828389
Cost function network-based design of protein-protein interactions: predicting changes in binding affinity, Bioinformatics, pp.733-750, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02154341
Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces, J. Comput. Biol, vol.25, p.29641249, 2018. ,
A hybrid Monte Carlo method for multibackbone protein design, J. Chem. Theory Comput, vol.12, pp.6035-6048, 2017. ,
Adaptive landscape flattening in amino acid sequence space for the computational design of protein:peptide binding, J. Chem. Phys, p.72302, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01975456
Monte Carlo simulations of proteins at constant pH with generalized Born solvent, flexible sidechains, and an effective dielectric boundary, J. Comput. Chem, vol.34, pp.2742-2756, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00984643
Comparing pairwise-additive and manybody generalized Born models for acid/base calculations and protein design, J. Comput. Chem, vol.38, pp.2396-2410, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01964492
Simulated annealing: Theory and applications ,
An object-oriented library for computational protein design, J. Comput. Chem, vol.28, pp.2378-2388, 2007. ,
Automatic protein design with all atom force fields by exact and heuristic optimization, J. Mol. Biol, vol.301, pp.713-736, 2000. ,
Computational protein design: software implementation, parameter optimization, and performance of a simple model, J. Comput. Chem, vol.29, pp.1092-1102, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00488192
Computational protein design: The proteus software and selected applications, J. Comput. Chem, vol.34, pp.2472-2484, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00868677
Computational methods for protein design and protein sequence variability: biased Monte Carlo and replica exchange, Chem. Phys. Lett, vol.401, pp.205-210, 2005. ,
Protein:ligand binding free energies: a stringent test for computational protein design, J. Comput. Chem, vol.37, pp.404-415, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01276168
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, Replica Exchange Monte Carlo, and a multistart, steepestdescent heuristic, J. Comput. Chem, vol.37, pp.1781-1793, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01445473
Probability and random processes, 2001. ,
Computational protein design as a cost function network optimization problem. Principles and Practice of Constraint Programming, pp.840-849, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01191320
A new framework for computational protein design through cost function network optimization, Bioinformatics, vol.29, pp.2129-2136, 2013. ,
Computational protein design as an optimization problem, Artif. Intell, vol.212, pp.59-79, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01268554
Fast search algorithms for computational protein design, J. Comput. Chem, pp.1048-1058, 2016. ,
A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta, J. Chem. Theory Comput, vol.11, pp.609-622, 2015. ,
,
he Rosetta All-Atom Energy Function for Macromolecular Modeling and Design ,
, J. Chem. Theory Comput, vol.13, pp.3031-3048, 2017.
A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions, Structure, vol.19, pp.844-858, 2011. ,
Guaranteed Discrete Energy Optimization on Large Protein Design Problems, J. Chem. Theory Comput, vol.11, pp.5980-5989, 2015. ,
Variable Neighborhood Search, Comput. Oper. Res, vol.24, pp.1097-1100, 1997. ,
The Framework of Computational Protein Design, Methods Mol. Biol, vol.1529, pp.3-19, 2017. ,
,
Anytime hybrid best-first search with tree decomposition for weighted CSP, International Conference on Principles and Practice of Constraint Programming, pp.12-29, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01198361
Multi-Language Evaluation of Exact Solvers in Graphical Model Discrete Optimization, Constraints, vol.21, pp.413-434, 2016. ,
Soft arc consistency revisited, Artif. Intell, vol.174, pp.449-478, 2010. ,
Limited discrepancy search, Proc. of IJCAI'95, pp.607-615, 1995. ,
Exploiting Tree Decomposition for Guiding Neighborhoods Exploration for VNS. RAIRO OR, vol.47, pp.91-123, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01024210
Limited Discrepancy AND/OR Search and Its Application to Optimization Tasks in Graphical Models, Proc. of IJCAI, pp.617-623, 2016. ,
Optimal speedup of Las Vegas algorithms, Proc. of TCS, pp.128-133, 1993. ,
Computational sidechain placement and protein mutagenesis with implicit solvent models, Proteins: Struct., Funct., Bioinf, vol.67, pp.853-867, 2007. ,
A New Approach to the Rapid Determination of Protein Side Chain Conformations, J. Biomol. Struct. Dyn, vol.8, p.1892586, 1991. ,
URL : https://hal.archives-ouvertes.fr/hal-00313445
Full Protein Sequence Redesign with an MMGBSA Energy Function, J. Chem. Theory Comput, vol.13, p.28886244, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01954913
Variable neighbourhood search: methods and applications, vol.4, pp.319-360, 2008. ,
, A. 3rd International Conference on Variable Neighborhood Search (VNS'14). Electronic Notes in Discrete Mathematics, vol.47, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01679171
Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL), Proteins: Struct., Funct., Bioinf, vol.82, pp.3177-3187 ,
Multistate approaches in computational protein design, Protein Sci, vol.21, pp.1241-1252, 2012. ,
Modern Biocatalysis: Advances Towards Synthetic Biological Systems, vol.32, p.88, 2018. ,
Replicated parallel strategies for decomposition guided VNS, Electronic Notes in Discrete Mathematics, vol.47, pp.93-100, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02088733
Computational design of fully overlapping coding schemes for protein pairs and triplets, Scientific Reports, vol.7, p.15873, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01961705