Literature DB >> 28013427

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.

Bradley Sherborne1, Veerabahu Shanmugasundaram2, Alan C Cheng3, Clara D Christ4, Renee L DesJarlais5, Jose S Duca6, Richard A Lewis7, Deborah A Loughney8, Eric S Manas9, Georgia B McGaughey10, Catherine E Peishoff11, Herman van Vlijmen11.   

Abstract

In May and August, 2016, several pharmaceutical companies convened to discuss and compare experiences with Free Energy Perturbation (FEP). This unusual synchronization of interest was prompted by Schrödinger's FEP+ implementation and offered the opportunity to share fresh studies with FEP and enable broader discussions on the topic. This article summarizes key conclusions of the meetings, including a path forward of actions for this group to aid the accelerated evaluation, application and development of free energy and related quantitative, structure-based design methods.

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Year:  2016        PMID： 28013427     DOI： 10.1007/s10822-016-9996-y

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  2 in total

1.  Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

Authors:  Lingle Wang; Yujie Wu; Yuqing Deng; Byungchan Kim; Levi Pierce; Goran Krilov; Dmitry Lupyan; Shaughnessy Robinson; Markus K Dahlgren; Jeremy Greenwood; Donna L Romero; Craig Masse; Jennifer L Knight; Thomas Steinbrecher; Thijs Beuming; Wolfgang Damm; Ed Harder; Woody Sherman; Mark Brewer; Ron Wester; Mark Murcko; Leah Frye; Ramy Farid; Teng Lin; David L Mobley; William L Jorgensen; Bruce J Berne; Richard A Friesner; Robert Abel
Journal:  J Am Chem Soc       Date:  2015-02-12       Impact factor: 15.419

2.  Calculation of the relative change in binding free energy of a protein-inhibitor complex.

Authors:  P A Bash; U C Singh; F K Brown; R Langridge; P A Kollman
Journal:  Science       Date:  1987-01-30       Impact factor: 47.728
  2 in total
  12 in total

1.  The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Authors:  Andrea Rizzi; Travis Jensen; David R Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M Henriksen; Bert L de Groot; Zoe Cournia; Alex Dickson; Julien Michel; Michael K Gilson; Michael R Shirts; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2020-01-27       Impact factor: 3.686

2.  Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort.

Authors:  Ying-Duo Gao; Yuan Hu; Alejandro Crespo; Deping Wang; Kira A Armacost; James I Fells; Xavier Fradera; Hongwu Wang; Huijun Wang; Brad Sherborne; Andreas Verras; Zhengwei Peng
Journal:  J Comput Aided Mol Des       Date:  2017-10-06       Impact factor: 3.686

3.  Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Authors:  David L Mobley; Caitlin C Bannan; Andrea Rizzi; Christopher I Bayly; John D Chodera; Victoria T Lim; Nathan M Lim; Kyle A Beauchamp; David R Slochower; Michael R Shirts; Michael K Gilson; Peter K Eastman
Journal:  J Chem Theory Comput       Date:  2018-10-30       Impact factor: 6.006

4.  Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

Authors:  Samuel C Gill; Nathan M Lim; Patrick B Grinaway; Ariën S Rustenburg; Josh Fass; Gregory A Ross; John D Chodera; David L Mobley
Journal:  J Phys Chem B       Date:  2018-03-12       Impact factor: 2.991

5.  Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.

Authors:  Hannah M Baumann; Vytautas Gapsys; Bert L de Groot; David L Mobley
Journal:  J Phys Chem B       Date:  2021-04-27       Impact factor: 2.991

6.  Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4.

Authors:  David W Wright; Shunzhou Wan; Christophe Meyer; Herman van Vlijmen; Gary Tresadern; Peter V Coveney
Journal:  Sci Rep       Date:  2019-04-12       Impact factor: 4.379

7.  Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.

Authors:  Martin S Engler; Bertrand Caron; Lourens Veen; Daan P Geerke; Alan E Mark; Gunnar W Klau
Journal:  Algorithms Mol Biol       Date:  2019-02-05       Impact factor: 1.405

8.  SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.

Authors:  Martin Amezcua; Léa El Khoury; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2021-01-04       Impact factor: 3.686

9.  Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.

Authors:  Antonia S J S Mey; Jordi Juárez Jiménez; Julien Michel
Journal:  J Comput Aided Mol Des       Date:  2017-11-13       Impact factor: 3.686

10.  Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors.

Authors:  Shunzhou Wan; Andrew Potterton; Fouad S Husseini; David W Wright; Alexander Heifetz; Maciej Malawski; Andrea Townsend-Nicholson; Peter V Coveney
Journal:  Interface Focus       Date:  2020-10-16       Impact factor: 3.906
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