Computational Protein Design Under a Given Backbone Structure with the ABACUS Statistical Energy Function

2016 ◽  
pp. 217-226 ◽  
Author(s):  
Peng Xiong ◽  
Quan Chen ◽  
Haiyan Liu
Keyword(s):  
Protein Design ◽  
Energy Function ◽  
Computational Protein Design ◽  
Backbone Structure

scholarly journals Computational protein design with backbone plasticity

2016 ◽  
Vol 44 (5) ◽  
pp. 1523-1529 ◽  
Author(s):  
James T. MacDonald ◽  
Paul S. Freemont
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Protein Structures ◽  
Search Space ◽  
Computational Protein Design ◽  
Artificial Enzymes ◽  
Backbone Flexibility ◽  
Artificial Proteins ◽  
Naturally Occurring ◽  
Backbone Structure

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process.

An Atomistic Statistically Effective Energy Function for Computational Protein Design

2016 ◽  
Vol 12 (8) ◽  
pp. 4146-4168 ◽  
Author(s):  
Christopher M. Topham ◽  
Sophie Barbe ◽  
Isabelle André
Keyword(s):  
Protein Design ◽  
Energy Function ◽  
Computational Protein Design ◽  
Effective Energy

Pairwise decomposition of an MMGBSA energy function for computational protein design

2014 ◽  
Vol 35 (18) ◽  
pp. 1371-1387 ◽  
Author(s):  
Thomas Gaillard ◽  
Thomas Simonson
Keyword(s):  
Protein Design ◽  
Energy Function ◽  
Computational Protein Design

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
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