Literature DB >> 26544598

FESetup: Automating Setup for Alchemical Free Energy Simulations.

Hannes H Loeffler1, Julien Michel2, Christopher Woods3.   

Abstract

FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

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Year:  2015        PMID： 26544598     DOI： 10.1021/acs.jcim.5b00368

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


  32 in total

Review 1.  Free Energy Calculations for Protein-Ligand Binding Prediction.

Authors:  Willem Jespers; Johan Åqvist; Hugo Gutiérrez-de-Terán
Journal:  Methods Mol Biol       Date:  2021

2.  The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Authors:  Yuan Hu; Brad Sherborne; Tai-Sung Lee; David A Case; Darrin M York; Zhuyan Guo
Journal:  J Comput Aided Mol Des       Date:  2016-08-01       Impact factor: 3.686

3.  Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.

Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

4.  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

5.  Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD.

Authors:  Wei Jiang; Christophe Chipot; Benoît Roux
Journal:  J Chem Inf Model       Date:  2019-08-27       Impact factor: 4.956

6.  Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E.

Authors:  Angana Ray; Navjeet Ahalawat; Jagannath Mondal
Journal:  Biophys J       Date:  2017-12-19       Impact factor: 4.033

7.  Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.

Authors:  Christina Schindler; Friedrich Rippmann; Daniel Kuhn
Journal:  J Comput Aided Mol Des       Date:  2017-09-12       Impact factor: 3.686

8.  CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.

Authors:  Seonghoon Kim; Hiraku Oshima; Han Zhang; Nathan R Kern; Suyong Re; Jumin Lee; Benoît Roux; Yuji Sugita; Wei Jiang; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2020-10-28       Impact factor: 6.006

9.  Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2021-02-02       Impact factor: 6.006

10.  Large scale relative protein ligand binding affinities using non-equilibrium alchemy.

Authors:  Vytautas Gapsys; Laura Pérez-Benito; Matteo Aldeghi; Daniel Seeliger; Herman van Vlijmen; Gary Tresadern; Bert L de Groot
Journal:  Chem Sci       Date:  2019-12-02       Impact factor: 9.825
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