About two geometric problems in computational structural biology - Lecture 1 | Vidéo | Carmin.tv

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About two geometric problems in computational structural biology - Lecture 1

By Frédéric Cazals

Appears in collection : 2022 - Francophone Computer Algebra Days - Journées nationales de calcul formel

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.

Information about the video

Date of recording 03/03/2022
Date of publication 17/03/2022
Institution CIRM
Licence CC BY NC ND
Language English
Audience Researchers
Director(s) Guillaume Hennenfent
Format MP4

Citation data

DOI 10.24350/CIRM.V.19894203
Cite this video Cazals, Frédéric (03/03/2022). About two geometric problems in computational structural biology - Lecture 1. CIRM. Audiovisual resource. DOI: 10.24350/CIRM.V.19894203
URL https://dx.doi.org/10.24350/CIRM.V.19894203

Domain(s)

Computation

Bibliography

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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