Fast search algorithms for computational protein design

Journal of Computational Chemistry
Seydou TraoréSophie Barbe

Abstract

One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state-of-the-art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitudes. Building up on this, we improved and injected CFN technology into the well-established CPD package Osprey to allow all Osprey CPD algorithms to benefit from associated speedups. Because Osprey fundamentally relies on the ability of A* to produce conformations in increasing order of energy, we defined new A* strategies combining CFN lower bounds, with new side-chain positioning-based branching scheme. Beyond the speedups obtained in the new A*-CFN combination, this novel branching scheme enables a much faster enumeration of suboptimal sequences, far beyond what is reachable without it. Together with the immediate and important speedups provided by CFN technology, these developments directly benefit to all the algorithms that previously relied on the DEE/ A* combination inside Osprey* and make it possible to solve larger CPD problems wit...Continue Reading

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Citations

Sep 30, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mark A HallenBruce R Donald
Apr 27, 2018·Expert Opinion on Drug Discovery·Dani SetiawanYang Zhang
Oct 15, 2019·Communications of the ACM·Mark A Hallen, Bruce R Donald
Dec 3, 2016·Essays in Biochemistry·Jana AupičRoman Jerala
Apr 12, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adegoke A OjewoleBruce R Donald
Aug 17, 2019·Nature Reviews. Molecular Cell Biology·Brian Kuhlman, Philip Bradley
Oct 22, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Elizabeth BrunkUrsula Rothlisberger
Jun 15, 2019·Bioinformatics·Jelena VucinicThomas Schiex
May 8, 2021·Protein Engineering, Design & Selection : PEDS·Younes BouchibaSophie Barbe
Jul 7, 2021·Proteins·François BeuvinDavid Simoncini
Nov 2, 2018·Journal of Chemical Information and Modeling·Antoine CharpentierDavid Allouche

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