Literature DB >> 31391883

Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Daniel J Cole1, Israel Cabeza de Vaca2, William L Jorgensen2.   

Abstract

A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.

Entities:  

Year:  2019        PMID： 31391883      PMCID： PMC6644397          DOI： 10.1039/c9md00017h

Source DB:  PubMed          Journal:  Medchemcomm        ISSN： 2040-2503            Impact factor:   3.597


  46 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

Authors:  Pu Liu; Byungchan Kim; Richard A Friesner; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-19       Impact factor: 11.205

Review 3.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

4.  Predicting absolute ligand binding free energies to a simple model site.

Authors:  David L Mobley; Alan P Graves; John D Chodera; Andrea C McReynolds; Brian K Shoichet; Ken A Dill
Journal:  J Mol Biol       Date:  2007-06-08       Impact factor: 5.469

5.  Intermolecular potentials.

Authors:  Anthony J Stone
Journal:  Science       Date:  2008-08-08       Impact factor: 47.728

6.  A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations.

Authors:  Frank R Beierlein; Julien Michel; Jonathan W Essex
Journal:  J Phys Chem B       Date:  2011-04-08       Impact factor: 2.991

Review 7.  Alchemical free energy methods for drug discovery: progress and challenges.

Authors:  John D Chodera; David L Mobley; Michael R Shirts; Richard W Dixon; Kim Branson; Vijay S Pande
Journal:  Curr Opin Struct Biol       Date:  2011-02-23       Impact factor: 6.809

8.  Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

Authors:  Lingle Wang; Richard A Friesner; B J Berne
Journal:  J Phys Chem B       Date:  2011-07-07       Impact factor: 2.991

9.  The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

Authors:  Emilio Gallicchio; Mauro Lapelosa; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2010-09-14       Impact factor: 6.006

Review 10.  Efficient drug lead discovery and optimization.

Authors:  William L Jorgensen
Journal:  Acc Chem Res       Date:  2009-06-16       Impact factor: 22.384
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  4 in total

1.  Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Authors:  David R Slochower; Niel M Henriksen; Lee-Ping Wang; John D Chodera; David L Mobley; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2019-10-25       Impact factor: 6.006

2.  Increasing the Potential of the Auristatin Cancer-Drug Family by Shifting the Conformational Equilibrium.

Authors:  Iris K Sokka; Filip S Ekholm; Mikael P Johansson
Journal:  Mol Pharm       Date:  2019-06-28       Impact factor: 4.939

3.  New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy.

Authors:  Thomas A Manz; Taoyi Chen; Daniel J Cole; Nidia Gabaldon Limas; Benjamin Fiszbein
Journal:  RSC Adv       Date:  2019-06-19       Impact factor: 4.036

4.  Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields.

Authors:  Alessandra Mattei; Richard S Hong; Hanno Dietrich; Dzmitry Firaha; Julian Helfferich; Yifei Michelle Liu; Kiran Sasikumar; Nathan S Abraham; Rajni Miglani Bhardwaj; Marcus A Neumann; Ahmad Y Sheikh
Journal:  J Chem Theory Comput       Date:  2022-08-05       Impact factor: 6.578
  4 in total

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