| Computational design of a self-assembling symmetrical β-propeller protein ARD Voet, H Noguchi, C Addy, D Simoncini, D Terada, S Unzai, SY Park, ... Proceedings of the National Academy of Sciences 111 (42), 15102-15107, 2014 | 136 | 2014 |
| Guaranteed discrete energy optimization on large protein design problems D Simoncini, D Allouche, S De Givry, C Delmas, S Barbe, T Schiex Journal of chemical theory and computation 11 (12), 5980-5989, 2015 | 70 | 2015 |
| A probabilistic fragment-based protein structure prediction algorithm D Simoncini, F Berenger, R Shrestha, KYJ Zhang PloS one 7 (7), e38799, 2012 | 56 | 2012 |
| Computational design of symmetrical eight-bladed β-propeller proteins H Noguchi, C Addy, D Simoncini, S Wouters, B Mylemans, L Van Meervelt, ... IUCrJ 6 (1), 46-55, 2019 | 39 | 2019 |
| Seven amino acid types suffice to create the core fold of RNA polymerase S Yagi, AK Padhi, J Vucinic, S Barbe, T Schiex, R Nakagawa, D Simoncini, ... Journal of the American Chemical Society 143 (39), 15998-16006, 2021 | 31 | 2021 |
| Fitness landscape analysis around the optimum in computational protein design D Simoncini, S Barbe, T Schiex, S Verel Proceedings of the Genetic and Evolutionary Computation Conference, 355-362, 2018 | 27 | 2018 |
| Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm D Simoncini, KYJ Zhang PLoS One 8 (7), e68954, 2013 | 27 | 2013 |
| Durandal: fast exact clustering of protein decoys F Berenger, R Shrestha, Y Zhou, D Simoncini, KYJ Zhang Journal of computational chemistry 33 (4), 471-474, 2012 | 27 | 2012 |
| Balancing exploration and exploitation in population‐based sampling improves fragment‐based de novo protein structure prediction D Simoncini, T Schiex, KYJ Zhang Proteins: Structure, Function, and Bioinformatics 85 (5), 852-858, 2017 | 26 | 2017 |
| Positive multistate protein design J Vucinic, D Simoncini, M Ruffini, S Barbe, T Schiex Bioinformatics 36 (1), 122-130, 2020 | 25 | 2020 |
| Guaranteed weighted counting for affinity computation: Beyond determinism and structure C Viricel, D Simoncini, S Barbe, T Schiex Principles and Practice of Constraint Programming: 22nd International …, 2016 | 25 | 2016 |
| On the influence of selection operators on performances in cellular genetic algorithms D Simoncini, P Collard, S Verel, M Clergue 2007 IEEE Congress on Evolutionary Computation, 4706-4713, 2007 | 23 | 2007 |
| Anisotropic selection in cellular genetic algorithms D Simoncini, S Verel, P Collard, M Clergue Proceedings of the 8th annual conference on Genetic and evolutionary …, 2006 | 22 | 2006 |
| Population-based sampling and fragment-based de novo protein structure prediction D Simoncini, KYJ Zhang Encyclopedia of Bioinformatics and Computational Biology-Reference Work 2019 …, 2019 | 21 | 2019 |
| Quality assessment of predicted protein models using energies calculated by the fragment molecular orbital method D Simoncini, H Nakata, K Ogata, S Nakamura, KYJ Zhang Molecular Informatics 34 (2‐3), 97-104, 2015 | 16 | 2015 |
| Evolution-inspired computational design of symmetric proteins ARD Voet, D Simoncini, JRH Tame, KYJ Zhang Computational protein design, 309-322, 2017 | 13 | 2017 |
| Centric selection: a way to tune the exploration/exploitation trade-off D Simoncini, S Verel, P Collard, M Clergue Proceedings of the 11th Annual conference on Genetic and evolutionary …, 2009 | 13 | 2009 |
| Approximate counting with deterministic guarantees for affinity computation C Viricel, D Simoncini, D Allouche, S De Givry, S Barbe, T Schiex Modelling, Computation and Optimization in Information Systems and …, 2015 | 12 | 2015 |
| Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing R Shrestha, D Simoncini, KYJ Zhang Acta Crystallographica Section D: Biological Crystallography 68 (11), 1522-1534, 2012 | 9 | 2012 |
| From cells to islands: An unified model of cellular parallel genetic algorithms D Simoncini, P Collard, S Verel, M Clergue International Conference on Cellular Automata, 248-257, 2006 | 9 | 2006 |
Thomas SchiexUniversité Fédérale de Toulouse, ANITI, INRAE, Toulouse, FranceVerified email at inrae.fr