Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

2011 ◽  
Vol 79 (12) ◽  
pp. 3448-3468 ◽  
Author(s):  
Savvas Polydorides ◽  
Najette Amara ◽  
Caroline Aubard ◽  
Pierre Plateau ◽  
Thomas Simonson ◽  
...  
Keyword(s):  
Protein Design ◽  
Trna Synthetase ◽  
Computational Protein Design ◽  
Model Application ◽  
Generalized Born ◽  
Solvent Model

scholarly journals Proteus software for physics-based protein design

2020 ◽  
Author(s):  
David Mignon ◽  
Karen Druart ◽  
Vaitea Opuu ◽  
Savvas Polydorides ◽  
Francesco Villa ◽  
...  
Keyword(s):  
Protein Design ◽  
Catalytic Efficiency ◽  
Trna Synthetase ◽  
Side Chain ◽  
Pdz Domains ◽  
Enzyme Design ◽  
Generalized Born ◽  
Binding Reaction ◽  
Unfolded State ◽  
Replica Exchange Monte Carlo

AbstractWe describe methods and software for physics-based protein design. The folded state energy combines molecular mechanics with Generalized Born solvent. Sequence and conformation space are sampled with Replica Exchange Monte Carlo, assuming one or a few fixed protein backbone structures and discrete side chain rotamers. Whole protein design and enzyme design are presented as illustrations. Full redesign of three PDZ domains was done using a simple, empirical, unfolded state model. Designed sequences were very similar to natural ones. Enzyme redesign exploited a powerful, adaptive, importance sampling approach that allows the design to directly target substrate binding, reaction rate, catalytic efficiency, or the specificity of these properties. Redesign of tyrosyl-tRNA synthetase stereospecificity is reported as an example.

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

Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design

2017 ◽  
Vol 38 (28) ◽  
pp. 2396-2410 ◽  
Author(s):  
Francesco Villa ◽  
David Mignon ◽  
Savvas Polydorides ◽  
Thomas Simonson
Keyword(s):  
Protein Design ◽  
Many Body ◽  
Acid Base ◽  
Generalized Born

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
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