Literature DB >> 31607753

Protein Design by Provable Algorithms.

Mark A Hallen1, Bruce R Donald2.   

Abstract

Entities:  

Year:  2019        PMID: 31607753      PMCID: PMC6788629          DOI: 10.1145/3338124

Source DB:  PubMed          Journal:  Commun ACM        ISSN: 0001-0782            Impact factor:   4.654


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  35 in total

1.  Guaranteed Discrete Energy Optimization on Large Protein Design Problems.

Authors:  David Simoncini; David Allouche; Simon de Givry; Céline Delmas; Sophie Barbe; Thomas Schiex
Journal:  J Chem Theory Comput       Date:  2015-11-25       Impact factor: 6.006

2.  New algorithms and an in silico benchmark for computational enzyme design.

Authors:  Alexandre Zanghellini; Lin Jiang; Andrew M Wollacott; Gong Cheng; Jens Meiler; Eric A Althoff; Daniela Röthlisberger; David Baker
Journal:  Protein Sci       Date:  2006-12       Impact factor: 6.725

3.  An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.

Authors:  Christina L Vizcarra; Naigong Zhang; Shannon A Marshall; Ned S Wingreen; Chen Zeng; Stephen L Mayo
Journal:  J Comput Chem       Date:  2008-05       Impact factor: 3.376

4.  Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm.

Authors:  A R Leach; A P Lemon
Journal:  Proteins       Date:  1998-11-01

5.  Protein design algorithms predict viable resistance to an experimental antifolate.

Authors:  Stephanie M Reeve; Pablo Gainza; Kathleen M Frey; Ivelin Georgiev; Bruce R Donald; Amy C Anderson
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-31       Impact factor: 11.205

6.  comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence.

Authors:  Mark A Hallen; Bruce R Donald
Journal:  J Comput Biol       Date:  2016-01-13       Impact factor: 1.479

Review 7.  Algorithms for protein design.

Authors:  Pablo Gainza; Hunter M Nisonoff; Bruce R Donald
Journal:  Curr Opin Struct Biol       Date:  2016-04-14       Impact factor: 6.809

8.  The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles.

Authors:  Ivelin Georgiev; Ryan H Lilien; Bruce R Donald
Journal:  J Comput Chem       Date:  2008-07-30       Impact factor: 3.376

9.  Fast search algorithms for computational protein design.

Authors:  Seydou Traoré; Kyle E Roberts; David Allouche; Bruce R Donald; Isabelle André; Thomas Schiex; Sophie Barbe
Journal:  J Comput Chem       Date:  2016-02-02       Impact factor: 3.376

10.  OSPREY 3.0: Open-source protein redesign for you, with powerful new features.

Authors:  Mark A Hallen; Jeffrey W Martin; Adegoke Ojewole; Jonathan D Jou; Anna U Lowegard; Marcel S Frenkel; Pablo Gainza; Hunter M Nisonoff; Aditya Mukund; Siyu Wang; Graham T Holt; David Zhou; Elizabeth Dowd; Bruce R Donald
Journal:  J Comput Chem       Date:  2018-10-14       Impact factor: 3.376

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  3 in total

1.  Computational Design of Miniprotein Binders.

Authors:  Younes Bouchiba; Manon Ruffini; Thomas Schiex; Sophie Barbe
Journal:  Methods Mol Biol       Date:  2022

Review 2.  Protein Design with Deep Learning.

Authors:  Marianne Defresne; Sophie Barbe; Thomas Schiex
Journal:  Int J Mol Sci       Date:  2021-10-29       Impact factor: 5.923

Review 3.  Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.

Authors:  Bartłomiej Surpeta; Carlos Eduardo Sequeiros-Borja; Jan Brezovsky
Journal:  Int J Mol Sci       Date:  2020-04-14       Impact factor: 5.923

  3 in total

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