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Record W4400555124 · doi:10.1021/acs.jpcb.4c01558

The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling

2024· article· en· W4400555124 on OpenAlexfundno aff
Lily Wang, Pavan Kumar Behara, Matthew W. Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey Wagner, Daniel J. Cole, Michael K. Gilson, Michael R. Shirts, David L. Mobley

Bibliographic record

VenueThe Journal of Physical Chemistry B · 2024
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicProtein Structure and Dynamics
Canadian institutionsnot available
FundersDivision of ChemistryNational Institute of General Medical SciencesOral and Maxillofacial Surgery FoundationBiotechnology and Biological Sciences Research CouncilYork UniversityNational Science Foundation
KeywordsField (mathematics)SoftwareForce field (fiction)Computer scienceFunction (biology)Work (physics)Data scienceComponent (thermodynamics)Key (lock)Software engineeringSystems engineeringEngineeringPhysicsMechanical engineeringArtificial intelligenceComputer securityMathematics

Abstract

fetched live from OpenAlex

Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.006
metaresearch head score (Gemma)0.014
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesOpen science
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Software · Consensus signal: none
Teacher disagreement score0.992
Threshold uncertainty score0.124

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0060.014
Meta-epidemiology (narrow)0.0020.002
Meta-epidemiology (broad)0.0020.003
Bibliometrics0.0030.004
Science and technology studies0.0020.002
Scholarly communication0.0040.007
Open science0.0080.006
Research integrity0.0060.008
Insufficient payload (model declined to judge)0.0370.017

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.016
GPT teacher head0.328
Teacher spread0.312 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
Domainnot available
GenreSoftware

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations31
Published2024
Admission routes1
Has abstractyes

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Same venueThe Journal of Physical Chemistry BSame topicProtein Structure and DynamicsFrench-language works237,207