scholarly journals A critical analysis of computational protein design with sparse residue interaction graphs

2017 ◽  
Vol 13 (3) ◽  
pp. e1005346 ◽  
Author(s):  
Swati Jain ◽  
Jonathan D. Jou ◽  
Ivelin S. Georgiev ◽  
Bruce R. Donald
Keyword(s):  
Protein Design ◽  
Critical Analysis ◽  
Computational Protein Design ◽  
Interaction Graphs ◽  
Residue Interaction

scholarly journals Iterated Local Search with Partition Crossover for Computational Protein Design

2021 ◽  
Author(s):  
François Beuvin ◽  
Simon de Givry ◽  
Thomas Schiex ◽  
Sébastien Verel ◽  
David Simoncini
Keyword(s):  
Local Search ◽  
Protein Design ◽  
Optimization Methods ◽  
Iterated Local Search ◽  
Biochemical Properties ◽  
Basins Of Attraction ◽  
Computational Protein Design ◽  
Local Minima ◽  
Search Optimization ◽  
Residue Interaction

Structure-based computational protein design (CPD) refers to the problem of finding a sequence of amino acids which folds into a specific desired protein structure, and possibly fulfills some targeted biochemical properties. Recent studies point out the particularly rugged CPD energy landscape, suggesting that local search optimization methods should be designed and tuned to easily escape local minima attraction basins. In this paper, we analyze the performance and search dynamics of an iterated local search (ILS) algorithm enhanced with partition crossover. Our algorithm, PILS, quickly finds local minima and escapes their basins of attraction by solution perturbation. Additionally, the partition crossover operator exploits the structure of the residue interaction graph in order to efficiently mix solutions and find new unexplored basins. Our results on a benchmark of 30 proteins of various topology and size show that PILS consistently finds lower energy solutions compared to Rosetta fixbb and a classic ILS, and that the corresponding sequences are mostly closer to the native.

scholarly journals cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design

2016 ◽  
Vol 23 (9) ◽  
pp. 737-749 ◽  
Author(s):  
Yuchao Pan ◽  
Yuxi Dong ◽  
Jingtian Zhou ◽  
Mark Hallen ◽  
Bruce R. Donald ◽  
...  
Keyword(s):  
Protein Design ◽  
Distributed Algorithm ◽  
Large Scale ◽  
Computational Protein Design

scholarly journals Discovery of Substrates for a SET Domain Lysine Methyltransferase Predicted by Multistate Computational Protein Design

Structure ◽  
2015 ◽  
Vol 23 (1) ◽  
pp. 206-215 ◽  
Author(s):  
Sylvain Lanouette ◽  
James A. Davey ◽  
Fred Elisma ◽  
Zhibin Ning ◽  
Daniel Figeys ◽  
...  
Keyword(s):  
Protein Design ◽  
Computational Protein Design ◽  
Set Domain ◽  
Lysine Methyltransferase

Electrostatics in computational protein design

2005 ◽  
Vol 9 (6) ◽  
pp. 622-626 ◽  
Author(s):  
Christina L Vizcarra ◽  
Stephen L Mayo
Keyword(s):  
Protein Design ◽  
Computational Protein Design

scholarly journals Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold

2011 ◽  
Vol 5 (1-2) ◽  
pp. 45-58 ◽  
Author(s):  
Doris J. Glykys ◽  
Géza R. Szilvay ◽  
Pablo Tortosa ◽  
María Suárez Diez ◽  
Alfonso Jaramillo ◽  
...  
Keyword(s):  
Protein Design ◽  
Computational Protein Design ◽  
Fungal Laccase ◽  
Synthetic Protein

Current methods and applications in computational protein design for food industry

2019 ◽  
Vol 60 (19) ◽  
pp. 3259-3270 ◽  
Author(s):  
Qiuming Chen ◽  
Yaqin Xiao ◽  
Wenli Zhang ◽  
Wanmeng Mu
Keyword(s):  
Protein Design ◽  
Food Industry ◽  
Computational Protein Design

Physics-Based Computational Protein Design: An Update

2020 ◽  
Vol 124 (51) ◽  
pp. 10637-10648
Author(s):  
David Mignon ◽  
Karen Druart ◽  
Eleni Michael ◽  
Vaitea Opuu ◽  
Savvas Polydorides ◽  
...  
Keyword(s):  
Protein Design ◽  
Computational Protein Design
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