Evidence map›Paper›PMID 36433835›Full record

ArticleJournal of chemical information and modeling2022

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.

Lorenzo D'Amore, David F Hahn, David L Dotson, Joshua T Horton, Jamshed Anwar, Ian Craig, Thomas Fox, Alberto Gobbi, Sirish Kaushik Lakkaraju, Xavier Lucas and 9 more

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. The Art and Science of Molecular Docking.Annual review of biochemistry · 2024
    Review
  11. Article
  12. Article
  13. Review
  14. Article
  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Lorenzo D'AmoreComputational Chemistry, Janssen R&D, C/Jarama 75A, 45007Toledo, Spain.ORCID 0000-0003-2245-1956
David F HahnComputational Chemistry, Janssen R&D, Turnhoutseweg 30, BeerseB-2340, Belgium.
David L DotsonThe Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States.
Joshua T HortonSchool of Natural and Environmental Sciences, Newcastle University, Newcastle upon TyneNE1 7RU, U.K.
Jamshed AnwarDepartment of Chemistry, Lancaster University, LancasterLA1 4YW, U.K.ORCID 0000-0003-1721-0330
Ian CraigMolecular Modeling & Drug Discovery, BASF SE, 67056Ludwigshafen, Germany.
Thomas FoxMedicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397Biberach/Riss, Germany.ORCID 0000-0002-1054-4701
Alberto GobbiGenentech, Inc., 1 DNA Way, South San Francisco, California94080, United States.ORCID 0000-0003-0434-9237
Sirish Kaushik LakkarajuSmall Molecule Drug Discovery, Bristol Myers Squibb, Princeton, New Jersey08540, United States.ORCID 0000-0003-1553-5780
Xavier LucasRoche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070Basel, Switzerland.ORCID 0000-0003-0887-3976
Katharina MeierComputational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789Monheim, Germany.
David L MobleyDepartments of Pharmaceutical Sciences and Chemistry, University of California, Irvine92617, United States.
Arjun NarayananData and Computational Sciences, Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Massachusetts02210, United States.
Christina E M SchindlerComputational Chemistry & Biologics, Merck KGaA, Frankfurter Strasse 250, 64293Darmstadt, Germany.ORCID 0000-0002-8980-048X
William C SwopeGenentech, Inc., 1 DNA Way, South San Francisco, California94080, United States.ORCID 0000-0002-5299-4145
Pieter J In 't VeldMolecular Modeling & Drug Discovery, BASF SE, 67056Ludwigshafen, Germany.ORCID 0000-0001-8460-5688
Jeffrey WagnerThe Open Force Field Initiative, Open Molecular Software Foundation, Davis, California95616, United States.
Bai XueXtalPi Inc. Floor 3, International Biomedical Innovation Park II, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, Guangdong518040, China.ORCID 0000-0002-8546-8096
Gary TresadernComputational Chemistry, Janssen R&D, Turnhoutseweg 30, BeerseB-2340, Belgium.ORCID 0000-0002-4801-1644

Funding

Mechanisms of Permeation and Gating of Voltage-Sensing DomainsR01GM098973 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI TOMBOLA, FRANCESCO · 2011 to 2025
$4.5M
Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug designR01GM132386 · NIGMS · UNIVERSITY OF COLORADO · PI SHIRTS, MICHAEL R · 2020 to 2023
$3.1M
Computational alchemy for molecular design and optimizationR01GM108889 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI MOBLEY, DAVID LOWELL · 2014 to 2022
$2.5M
Advancing predictive physical modeling through focused development of model systems to drive new modeling innovationsR01GM124270 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI MOBLEY, DAVID LOWELL · 2018 to 2021
$1.5M
NIGMS NIH HHS R01 GM098973NIGMS NIH HHS R01 GM108889NIGMS NIH HHS R01 GM124270NIGMS NIH HHS R01 GM132386
6 · The paper itself

Abstract

Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

Indexed as

ProteinsLigandsPhysical PhenomenaThermodynamicsLigandsProteins

Identifiers

PMID36433835
PMCPMC9873353

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.