Faculty Opinions recommendation of Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles.

2011 ◽  
Author(s):  
Brian Kuhlman ◽  
Gurkan Guntas
Keyword(s):  
Protein Design ◽  
Computational Protein Design ◽  
Library Screening ◽  
Structural Ensembles

scholarly journals rstoolbox: management and analysis of computationally designed structural ensembles

2018 ◽  
Author(s):  
Jaume Bonet ◽  
Zander Harteveld ◽  
Fabian Sesterhenn ◽  
Andreas Scheck ◽  
Bruno E. Correia
Keyword(s):  
Protein Design ◽  
Experimental Validation ◽  
Computational Protein Design ◽  
Design Tools ◽  
Link Type ◽  
New Approaches ◽  
Structural Ensembles ◽  
Effective Selection ◽  
Proper Analysis ◽  
Selection Of

AbstractMotivationComputational protein design (CPD) calculations rely on the generation of large amounts of data on the search for the best sequences. As such, CPD workflows generally include the batch generation of designed decoys (sampling) followed by ranking and filtering stages to select those with optimal metrics (scoring). Due to these factors, the proper analysis of the decoy population is a key element for the effective selection of designs for experimental validation.ResultsHere, we present a set of tools for the analysis of protein design ensembles. The tool is oriented towards protein designers with basic coding training aiming to process efficiently their decoy sets as well as for protocol developers interested in benchmarking their new approaches. Although initially devised to process Rosetta design outputs, the library is extendable to other design tools.Availability and Implementationrstoolbox is implemented for python2.7 and 3.5+. Code is freely available athttps://github.com/lpdi-epfl/rstoolboxunder the MIT license. Full documentation and examples can be found athttps://lpdi-epfl.github.io/rstoolbox.

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
Sign in / Sign up

Export Citation Format

Share Document