[{"command":"insert","method":null,"selector":".course-modal-ajax-placeholder-959345","data":"\u003Cdiv class=\u0022container content-rte\u0022\u003E\n  \u003Cdiv class=\u0022row\u0022\u003E\n    \u003Cdiv class=\u0022box col-md-6 bg-primary text-white\u0022\u003E\n      \u003Ch2 class=\u0022h1 text-left\u0022\u003E  Computational Protein Design\n\u003C\/h2\u003E\n                  \u003Cdiv class=\u0022field-spacing\u0022\u003E\n        \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EECTS :\n          2.5\n        \u003C\/div\u003E\n      \u003C\/div\u003E\n                  \u003Cdiv class=\u0022field-spacing\u0022\u003E\n        \u003Cdiv class=\u0022field__label h3 dash\u0022\u003ESemestre calendaire :\n          Semester 1\n        \u003C\/div\u003E\n      \u003C\/div\u003E\n            \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003ED\u00e9tail du volume horaire\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                          \u003Cspan class=\u0022field__label h4 mt-5 \u0022\u003ECours magistraux :\u003C\/span\u003E\n                                      \u003Cspan\u003E12\u003C\/span\u003E\n                      \u003C\/div\u003E\n                                              \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                          \u003Cspan class=\u0022field__label h4 mt-5 \u0022\u003ETravaux dirig\u00e9s :\u003C\/span\u003E\n                                      \u003Cspan\u003E8\u003C\/span\u003E\n                      \u003C\/div\u003E\n                                                            \u003C\/div\u003E\n        \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003ELangue d\u0026#039;enseignement\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003EAnglais\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n        \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EEnseignement \u00e0 distance\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003Enon\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n      \u003C\/div\u003E\n    \u003Cdiv class=\u0022box col-md-6\u0022\u003E\n            \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EPr\u00e9requis\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003E\u003Cp\u003EThe course prerequisites are a basic knowledge of molecular and structural biology, bioinformatics and thermodynamics.\u003C\/p\u003E\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n                \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EObjectifs d\u0026#039;apprentissage\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003E\u003Cp\u003EThis course provides an overview of the techniques used in computational protein design, from molecular modelling to in silico combinatorial library design, including those practical aspects associated with the integration of such computational techniques into a protein engineering project.\u003C\/p\u003E\n\u003Cp\u003EThe course covers various aspects of the field, including an overview of protein molecular modelling and dynamics, protein activity modelling, protein engineering, and protein design techniques:\u003C\/p\u003E\n\u003Cp\u003E- Molecular modelling: atomistic, descriptor-based, and knowledge-based models; solvent representations, AI for protein structure prediction.\u003C\/p\u003E\n\u003Cp\u003E- Force field-based techniques: energy minimization and molecular dynamics.\u003C\/p\u003E\n\u003Cp\u003E- Docking techniques: protein-protein, protein-peptide,\u0026nbsp; and protein-small molecule interactions.\u003C\/p\u003E\n\u003Cp\u003E- Descriptor-based modelling of biological activities: quantitative structure-activity relationship models.\u003C\/p\u003E\n\u003Cp\u003E- Knowledge-based modelling: rotamer libraries, large-scale analysis of propensities.\u003C\/p\u003E\n\u003Cp\u003E- Machine-learning and deep learning modeling.\u003C\/p\u003E\n\u003Cp\u003E- Protein design: search algorithms, combinatorial optimization, and library design.\u003C\/p\u003E\n\u003Cp\u003E- Design of protein-based properties\u0026nbsp; for synthetic biology applications: novel enzymatic, regulatory, and signalling activities.\u003C\/p\u003E\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n        \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EOrganisation g\u00e9n\u00e9rale et modalit\u00e9s p\u00e9dagogiques\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003E\u003Cp\u003EThe course is organised in 6 sessions:\u003C\/p\u003E\n\u003Cp\u003E1. Introduction to molecular modelling\u003C\/p\u003E\n\u003Cp\u003E2. Modelling biological activity of molecular structures\u003C\/p\u003E\n\u003Cp\u003E3. Introduction to biomolecular design\u003C\/p\u003E\n\u003Cp\u003E4. Hands-on exercise on computational tools for protein design.\u003C\/p\u003E\n\u003Cp\u003E5. Modelling protein interactions through docking techniques\u003C\/p\u003E\n\u003Cp\u003E6. Hands-on exercise on computational tools for molecular docking.\u003C\/p\u003E\n\u003Cp\u003EEvaluation: The course will be evaluated through two practical projects on computational molecular modelling (protein design and docking). The projects will be organised in groups of 1 or 2 students. Each team will write a report detailing the methodology used in the project and the obtained results.\u003C\/p\u003E\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n                        \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003EBibliographie\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003E\u003Cp\u003E- Carbonell P, Trosset JY. Computational protein design methods for synthetic biology. Methods Mol\u0026nbsp; Biol. 2015, 1244:3-21.\u003C\/p\u003E\n\u003Cp\u003E- Gainza-Cirauqui P, Correia BE. Computational protein design-the next generation tool to expand synthetic biology applications. Curr Opin Biotechnol. 2018, 52:145-152.\u003C\/p\u003E\n\u003Cp\u003E- Samish I. The Framework of Computational Protein Design. Methods Mol Biol. 2017, 1529:3-19\u003C\/p\u003E\n\u003Cp\u003E- Bagdad Y, Sisquellas M, Arthur M, Miteva MA. Machine Learning and Deep Learning Models for Predicting Noncovalent Inhibitors of AmpC \u03b2-Lactamase.\u0026nbsp;ACS Omega. 2024;9(40):41334-41342.\u0026nbsp;\u003C\/p\u003E\n\u003Cp\u003E- Gyulkhandanyan A, Rezaie AR, Roumenina L, Lagarde N, Fremeaux-Bacchi V, Miteva MA, Villoutreix BO.\u0026nbsp; Analysis of protein missense alterations by combining sequence- and structure-based methods.\u0026nbsp;Mol Genet Genomic Med. 2020 Apr;8(4):e1166.\u0026nbsp;\u003C\/p\u003E\n\u003Cp\u003E-\u0026nbsp; Rey J, Murail S, de Vries S, Derreumaux P, Tuffery P.\u0026nbsp; PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.\u0026nbsp;Nucleic Acids Res. 2023 Jul 5;51(W1):W432-W437.\u003C\/p\u003E\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n        \u003Cdiv class=\u0022field-spacing\u0022\u003E\n      \u003Cdiv class=\u0022field__label h3 dash\u0022\u003ENature de l\u0026#039;\u00e9valuation\u003C\/div\u003E\n                        \u003Cdiv class=\u0022mt-5 text-justify\u0022\u003E\n                                      \u003Cspan\u003EEvaluation Continue non Int\u00e9grale\u003C\/span\u003E\n                      \u003C\/div\u003E\n                  \u003C\/div\u003E\n      \u003C\/div\u003E\n  \u003C\/div\u003E\n\u003C\/div\u003E\n","settings":null}]