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OpenMM specifications

Information


Unique identifier OMICS_14094
Name OpenMM
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
Computer skills Advanced
Version 7.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Peter Eastman

Publications for OpenMM

OpenMM citations

 (36)
library_books

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

2018
PLoS One
PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] field for the protein degrees of freedom [], the gaff force field for the ligand degrees of freedom [], and the obc2 generalized-born implicit solvent model [,]. simulations were performed using the openmm simulation library [] with a non-bonded cut-off of 1 nanometer, a salt concentration of 150 mm, and hydrogen bond lengths constrained. equations of motion were integrated with a langevin […]

library_books

Phosphorylation induced cochaperone unfolding promotes kinase recruitment and client class specific Hsp90 phosphorylation

2018
Nat Commun
PMCID: 5772613
PMID: 29343704
DOI: 10.1038/s41467-017-02711-w

[…] initial structures of the helical core (residues 290–343) of the c-terminal domain of cdc37 were taken from the protein data bank (pdb id 2n5x). systems were built using charmm, but run with openmm using the charmm force field. three different systems were modeled, the unphosphorylated and y298 phosphorylated wild types, and the y298e mutant. systems were solvated in tip3p water boxes, […]

library_books

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation

2018
eLife
PMCID: 5849412
PMID: 29465396
DOI: 10.7554/eLife.32766.019

[…] only heavy atoms) was extracted from the structure and converted to a protonated tripos mol2 file using openeye toolkit oechem v2015.june (; ). the protein structure was then loaded as an openmm version 7.0.1 modeller object, and the protonated adp was reintroduced through conversion from mol2 to openmm format via mdtraj 1.4.2 (; )., simulations of phosphorylated wt aura in complex […]

library_books

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

2018
eLife
PMCID: 5896879
PMID: 29638214
DOI: 10.7554/eLife.32963.032

[…] or dnacaa; the dna sequence used in the simulations contained nucleotides g5 – c18 from the crystal structure. the charmm 36 forcefield (; ; ; ; ) and charmm program (), with the charmm interface to openmm () to allow the use of nvidia graphical processing units (gpus), were used for all simulations. the starting structure was placed in a cubic solvent box with 8 nm side length containing water […]

library_books

A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture

2017
PMCID: 5730859
PMID: 29217590
DOI: 10.15252/embj.201798083

[…] t al, )., polymer simulations of loop extrusion were performed as in flyamer et al (), but using updates to the simulation engine (fudenberg & imakaev, ). the simulation engine is built using the openmm‐polymer package which relies on openmm 7 (eastman et al, ). parameters for simulations were as follows: 2,000 md steps per loop extrusion step. simulations were performed using either n = 30,00 […]

library_books

Millisecond dynamics of BTK reveal kinome wide conformational plasticity within the apo kinase domain

2017
Sci Rep
PMCID: 5688120
PMID: 29142210
DOI: 10.1038/s41598-017-10697-0

[…] counter ions. the amber99sb-ildn force field was used to model protein dynamics in conjunction with the tip3p water model. the structures were minimized in two steps using amber and then loaded into openmm for npt production runs on [email protected] overall we generated 1.7ms of aggregate data for both ensembles., building a msm requires identification of metastable kinetically similar states. […]


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OpenMM institution(s)
Department of Chemistry, Stanford University, Stanford, CA, USA; Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, USA; Computational Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Counsyl Research, South San Francisco, CA, USA; Department of Chemistry, University of California, Davis, CA, USA; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
OpenMM funding source(s)
This was supported by the NIH Roadmap for Medical Research Grant U54 GM072970, NIH grant R01-GM062868, the Sloan Kettering Institute, NIH grant P30 CA008748, and Starr Foundation grant I8-A8-058.

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