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About two geometric problems in computational structural biology - Lecture 1
Multi angle
Authors : Cazals, Frédéric (Author of the conference)
CIRM (Publisher )
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 (Publisher )
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Abstract :
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.
Keywords : molecular geometry; tripeptides; molecular conformations; kinetic data structures; thermodynamics; polytopes; volumes; randomized algorithms
MSC Codes : Keywords : 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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Information on the Video
Film maker : Hennenfent, GuillaumeLanguage : English Available date : 17/03/2022 Conference Date : 03/03/2022 Subseries : Research School arXiv category : Computation Mathematical Area(s) : Algebra ; Computer Science ; Geometry Format : MP4 (.mp4) - HD Video Time : 01:38:12 Targeted Audience : Researchers ; Doctoral Students, Post-Doctoral Students Download : https://videos.cirm-math.fr/2022-03-03_Cazals_Part1.mp4 
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Information on the Event
Event Title : Francophone Computer Algebra Days / JNCF - Journées nationales de calcul formelEvent Organizers : Boito, Paola ; Guerrini, Eleonora ; Koseleff, Pierre-Vincent ; Spaenlehauer, Pierre-Jean ; Vaccon, Tristan Dates : 28/02/2022 - 04/03/2022 Event Year : 2022 Event URL : https://conferences.cirm-math.fr/2568.html
Citation Data
DOI : 10.24350/CIRM.V.19894203Cite this video as: 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 |
See Also
- [Multi angle] Validated symbolic-numeric algorithms and practical applications in aerospace - Lecture 2 / Author of the conference Joldes, Mioara.
- [Multi angle] Effective aspects of the geometry of tensors - Lecture 2 / Author of the conference Ottaviani, Giorgio.
- [Multi angle] Effective aspects of the geometry of tensors - Lecture 1 / Author of the conference Ottaviani, Giorgio.
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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