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About two geometric problems in computational structural biology - Lecture 1

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Auteurs : Cazals, Frédéric (Auteur de la conférence)
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 :
46N55 - Applications in statistical physics
65D18 - Computer graphics, image analysis, and computational geometry
92E10 - Molecular structure (graph-theoretic methods, methods of differential topology, etc.)

    Informations sur la Vidéo

    Réalisateur : Hennenfent, Guillaume
    Langue : 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

Informations sur la Rencontre

Nom de la Rencontre : Francophone Computer Algebra Days / JNCF - Journées nationales de calcul formel
Organisateurs 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.19894203
Citer 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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