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Appears in collection : 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.

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Citation data

  • DOI 10.24350/CIRM.V.19894203
  • Cite this video Cazals Frédéric (3/3/22). 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

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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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