Evidence map›Paper›PMID 38958156›Full record

ArticleThe Journal of chemical physics2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.

Rose A Gogal, Aaron J Nessler, Andrew C Thiel, Hernan V Bernabe, Rae A Corrigan Grove, Leah M Cousineau, Jacob M Litman, Jacob M Miller, Guowei Qi, Matthew J Speranza and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of chemical physics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

21 authors.

Rose A GogalRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0001-9550-6415
Aaron J NesslerRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0009-0004-2502-6204
Andrew C ThielRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-8652-3042
Hernan V BernabeRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.
Rae A Corrigan GroveTheoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.ORCID 0000-0003-3628-9347
Leah M CousineauDepartment of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA.
Jacob M LitmanDepartment of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-3256-8747
Jacob M MillerRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-1999-4282
Guowei QiDepartment of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-0005-7387
Matthew J SperanzaRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0009-0000-1372-0160
Mallory R TollefsonRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-4750-5554
Timothy D FennAnalytical Development, LEXEO Therapeutics, New York, New York 10010, USA.ORCID 0009-0007-5663-5303
Jacob J MichaelsonDepartment of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA.ORCID 0000-0001-9713-0992
Okimasa OkadaSohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan.ORCID 0000-0002-1841-5429
Jean-Philip PiquemalDepartment of Chemistry, Sorbonne Université, F-75005 Paris, France.ORCID 0000-0001-6615-9426
Jay W PonderDepartment of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA.ORCID 0000-0001-5450-9230
Jana ShenDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA.ORCID 0000-0002-3234-0769
Richard J H SmithMolecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA.ORCID 0000-0003-1201-6731
Wei YangRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0002-4520-3253
Pengyu RenDepartment of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA.ORCID 0000-0002-5613-1910
Michael J SchniedersRoy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.ORCID 0000-0003-1260-4592

Funding

Optimizing Genetic Testing for Deafness for Clinical DiagnosticsR01DC012049 · NIDCD · UNIVERSITY OF IOWA · PI TERRY A BRAUN, Thomas L. Casavant · 2011 to 2026
$8.7M
DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELDR01GM106137 · NIGMS · WASHINGTON UNIVERSITY · PI JAY PONDER, Pengyu Ren · 2013 to 2026
$3.5M
Specificity and Selectivity in Protein-Ion BindingR01GM114237 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI PONDER, JAY, REN, PENGYU · 2015 to 2023
$2.6M
Molecular mechanisms of proton-coupled dynamic processes in biologyR35GM148261 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE · PI Jana Shen · 2023 to 2026
$1.5M
Free Energy Sampling of Long-Timescale Biomolecular DynamicsR01GM124621 · NIGMS · FLORIDA STATE UNIVERSITY · PI YANG, WEI · 2020 to 2023
$1.4M
NIDCD NIH HHS R01 DC012049NIGMS NIH HHS R01 GM106137NIGMS NIH HHS R01 GM114237NIGMS NIH HHS R01 GM124621NIGMS NIH HHS R35 GM148261
6 · The paper itself

Abstract

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

Indexed as

SoftwareAlgorithmsCrystallizationGenetic VariationMolecular Dynamics SimulationNucleic AcidsProteinsThermodynamicsNucleic AcidsProteins

Identifiers

PMID38958156
PMCPMC11223778

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.