CITATION.cff

cff-version: 1.2.0
title: OpenFF BespokeFit
message: >-
  In any publications using force fields produced by
  BespokeFit, please cite:
type: software
authors:
  - given-names: The BespokeFit Contributors
identifiers:
  - type: doi
    value: 10.1021/acs.jcim.2c01153
  - type: url
    value: 'https://doi.org/10.26434/chemrxiv-2022-6h628'
    description: ChemRxiv
repository-code: 'https://github.com/openforcefield/openff-bespokefit'
url: 'https://docs.openforcefield.org/bespokefit'
abstract: >-
  The development of accurate transferable force fields is
  key to realizing the full potential of atomistic modeling
  in the study of biological processes such as
  protein–ligand binding for drug discovery.
  State-of-the-art transferable force fields, such as those
  produced by the Open Force Field Initiative, use modern
  software engineering and automation techniques to yield
  accuracy improvements. However, force field torsion
  parameters, which must account for many stereoelectronic
  and steric effects, are considered to be less transferable
  than other force field parameters and are therefore often
  targets for bespoke parametrization. Here, we present the
  Open Force Field QCSubmit and BespokeFit software packages
  that, when combined, facilitate the fitting of torsion
  parameters to quantum mechanical reference data at scale.
  We demonstrate the use of QCSubmit for simplifying the
  process of creating and archiving large numbers of quantum
  chemical calculations, by generating a dataset of 671
  torsion scans for druglike fragments. We use BespokeFit to
  derive individual torsion parameters for each of these
  molecules, thereby reducing the root-mean-square error in
  the potential energy surface from 1.1 kcal/mol, using the
  original transferable force field, to 0.4 kcal/mol using
  the bespoke version. Furthermore, we employ the bespoke
  force fields to compute the relative binding free energies
  of a congeneric series of inhibitors of the TYK2 protein,
  and demonstrate further improvements in accuracy, compared
  to the base force field (MUE reduced from
  0.56_{0.39}^{0.77} to 0.42_{0.28}^{0.59} kcal/mol and R2
  correlation improved from 0.72_{0.35}^{0.87} to
  0.93_{0.84}^{0.97}).
keywords:
  - force field
  - free energy
  - molecular mechanics
  - forcebalance
  - openff
  - smirnoff
  - qcsubmit
  - qcengine
license: MIT

preferred-citation:
  type: article
  title: >-
    Open Force Field BespokeFit: Automating Bespoke Torsion
    Parametrization at Scale
  authors:
    - given-names: Joshua T.
      family-names: Horton
      orcid: 'https://orcid.org/0000-0001-8694-7200'
      affiliation: >-
        School of Natural and Environmental Sciences,
        Newcastle University
    - given-names: Simon
      family-names: Boothroyd
      affiliation: Boothroyd Scientific Consulting Ltd.
      orcid: 'https://orcid.org/0000-0002-3456-1872'
    - given-names: Jeffrey
      family-names: Wagner
      affiliation: The Open Force Field Initiative
      orcid: 'https://orcid.org/0000-0001-6448-0873'
    - given-names: Joshua A.
      family-names: Mitchell
      affiliation: The Open Force Field Initiative
      orcid: 'https://orcid.org/0000-0002-8246-5113'
      email: josh.mitchell@openforcefield.org
    - given-names: Trevor
      family-names: Gokey
      affiliation: 'Dept. Chemistry, UC Irvine'
      orcid: 'https://orcid.org/0000-0001-7856-1156'
    - given-names: David L.
      family-names: Dotson
      orcid: 'https://orcid.org/0000-0001-5879-2942'
      affiliation: The Open Force Field Initiative
    - given-names: Pavan Kumar
      family-names: Behara
      orcid: 'https://orcid.org/0000-0001-6583-2148'
      affiliation: 'Dept. Pharmaceutical Sciences, UC Irvine'
    - given-names: Venkata Krishnan
      family-names: Ramaswamy
      affiliation: Cresset BioMolecular Discovery Ltd.
      orcid: 'https://orcid.org/0000-0002-5804-8483'
    - given-names: Mark
      family-names: Mackey
      affiliation: Cresset BioMolecular Discovery Ltd.
      orcid: 'https://orcid.org/0000-0001-5131-7583'
    - orcid: 'https://orcid.org/0000-0003-0542-119X'
      given-names: John D.
      family-names: Chodera
      affiliation: >-
        Computational & Systems Biology Program, Sloan
        Kettering Institute
    - given-names: Jamshed
      family-names: Anwar
      affiliation: 'Dept. Chemistry, Lancaster University'
      orcid: 'https://orcid.org/0000-0003-1721-0330'
    - given-names: David L.
      family-names: Mobley
      affiliation: 'Dept. Chemistry, UC Irvine'
      orcid: 'https://orcid.org/0000-0002-1083-5533'
    - given-names: Daniel J.
      family-names: Cole
      affiliation: >-
        School of Natural and Environmental Sciences,
        Newcastle University
      orcid: 'https://orcid.org/0000-0003-2933-0719'
      email: daniel.cole@ncl.ac.uk
  identifiers:
    - type: doi
      value: 10.1021/acs.jcim.2c01153
    - type: url
      value: 'https://doi.org/10.26434/chemrxiv-2022-6h628'
      description: ChemRxiv Pre-Print
  doi: "10.1021/acs.jcim.2c01153"
  journal: "J. Chem. Inf. Model."
  month: 11
  start: 5622 # First page number
  end: 5633 # Last page number
  issue: 22
  volume: 62
  year: 2022