English
About two geometric problems in computational structural biology - Lecture 1
Multi angle
Auteurs : Cazals, Frédéric (Auteur de la conférence)
CIRM (Editeur )
46N55 - Applications in statistical physics
65D18 - Computer graphics, image analysis, and computational geometry
92E10 - Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
CIRM (Editeur )
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Résumé :
Proteins are flexible molecules involved in all biological functions. Understanding these functions actually requires delving into protein structure, thermodynamics, and kinetics. This talk will be devoted to two problems in this area. The first one is the (uniform) generation of conformations of a protein backbone in the so-called rigid geometry model. We will present a method based on algebraic solutions of the so-called tripeptide loop closure. The second one deals with the calculation of the volume of high dimensional polytope, a questions closely related to the computation of density of states in statistical physics.
Mots-Clés : molecular geometry; tripeptides; molecular conformations; kinetic data structures; thermodynamics; polytopes; volumes; randomized algorithms
Codes MSC : Mots-Clés : molecular geometry; tripeptides; molecular conformations; kinetic data structures; thermodynamics; polytopes; volumes; randomized algorithms
46N55 - Applications in statistical physics
65D18 - Computer graphics, image analysis, and computational geometry
92E10 - Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
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Informations sur la Vidéo
Réalisateur : Hennenfent, GuillaumeLangue : Anglais Date de Publication : 17/03/2022 Date de Captation : 03/03/2022 Sous Collection : Research School Catégorie arXiv : Computation Domaine(s) : Algèbre ; Informatique ; Géométrie Format : MP4 (.mp4) - HD Durée : 01:38:12 Audience : Chercheurs ; Doctoral Students, Post-Doctoral Students Download : https://videos.cirm-math.fr/2022-03-03_Cazals_Part1.mp4 
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Informations sur la Rencontre
Nom de la Rencontre : Francophone Computer Algebra Days / JNCF - Journées nationales de calcul formelOrganisateurs de la Rencontre : Boito, Paola ; Guerrini, Eleonora ; Koseleff, Pierre-Vincent ; Spaenlehauer, Pierre-Jean ; Vaccon, Tristan Dates : 28/02/2022 - 04/03/2022 Année de la rencontre : 2022 URL de la Rencontre : https://conferences.cirm-math.fr/2568.html
Données de citation
DOI : 10.24350/CIRM.V.19894203Citer cette vidéo: Cazals, Frédéric (2022). About two geometric problems in computational structural biology - Lecture 1. CIRM. Audiovisual resource. doi:10.24350/CIRM.V.19894203 URI : http://dx.doi.org/10.24350/CIRM.V.19894203 |
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Bibliographie
- COUTSIAS, Evangelos A., SEOK, Chaok, JACOBSON, Matthew P., et al. A kinematic view of loop closure. Journal of computational chemistry, 2004, vol. 25, no 4, p. 510-528. - https://doi.org/10.1002/jcc.10416
- O'DONNELL, Timothée, ROBERT, Charles H., et CAZALS, Frédéric. Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics, 2022, vol. 90, no 3, p. 858-868. - https://doi.org/10.1002/prot.26281
- O'DONNELL, Timothée et CAZALS, Frédéric. Geometric constraints within tripeptides and the existence of tripeptide reconstructions. To appear. -
- O'DONNELL, Timothée et CAZALS, Frédéric. Protein loops sampling based on a global parameterization of the backbone conformational space. To appear. -
- CHEVALLIER, Augustin, CAZALS, Frédéric, et FEARNHEAD, Paul. Efficient computation of the volume of a polytope in high-dimensions using Piecewise Deterministic Markov Processes. arXiv preprint arXiv:2202.09129, 2022. - https://arxiv.org/abs/2202.09129
- CHEVALLIER, Augustin, PION, Sylvain, et CAZALS, Frédéric. Improved polytope volume calculations based on Hamiltonian Monte Carlo with boundary reflections and sweet arithmetics. Journal of Computational Geometry, NA (NA), 2022. -
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