Comparison of nucleic acid simulation software

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This is a list of notable computer programs that are used for nucleic acids simulations.

Name View 3D Model build Min MD MC REM Crt Int Exp Imp Lig GPU Comments License Website
Abalone Yes Yes Yes Yes Yes Yes Yes No Yes Yes Yes Yes DNA, proteins, ligands Free Agile Molecule
AMBER[1] No Yes Yes Yes No Yes Yes No Yes Yes Yes Yes[2] AMBER force field Proprietary ambermd.org
Ascalaph Designer Yes Yes Yes Yes No No Yes No Yes Yes Yes No AMBER Free, GPL biomolecular-modeling.com
CHARMM No Yes Yes Yes Yes No Yes No Yes Yes Yes No CHARMM force field Proprietary charmm.org
CP2K No No Yes Yes Yes Yes Yes No Yes No No Yes Free, GPL cp2k.org
Forecaster (Fitted)[3] Yes No Yes No No No Yes No Yes No Yes No Small molecule docking to nucleic acids with water placement Free for academia, Proprietary Molecular Forecaster Archived 2019-07-09 at the Wayback Machine
ICM[4] Yes Yes Yes No Yes No No Yes No Yes No No Global optimization Proprietary Molsoft
JUMNA[5] No Yes Yes No No No No Yes No Yes No No Proprietary
MDynaMix[6] Yes Yes No Yes No No Yes No Yes No Yes No Common MD Free, GPL Stockholm University
Molecular Operating Environment (MOE) Yes Yes Yes Yes No No Yes No Yes No Yes No Proprietary Chemical Computing Group
Nucleic Acid Builder (NAB)[7] No Yes No No No No No No No No No No Generates models for unusual DNA, RNA Free, GPL New Jersey University
NAnoscale Molecular Dynamics (NAMD) Yes No Yes Yes No No Yes No Yes No Yes Yes Fast, parallel MD, CUDA Free University of Illinois
oxDNA[8][9] Yes Yes Yes Yes Yes Yes Yes No No Yes No Yes Coarse-grained models of DNA, RNA Free, GPL dna.physics.ox.ac.uk

LAMMPS CG-DNA

QRNAS [10] No No Yes No No No Yes No No Yes No No High resolution refinement of models of RNA, DNA and hybrids using AMBER force field . Free, GPL Genesilico Github
SimRNA[11] Yes Yes No No Yes Yes Yes Yes No Yes No No Coarse grained modeling of RNA Free for Academic, Proprietary Genesilico
SimRNAweb[12] Yes Yes No No Yes Yes Yes Yes No Yes No No Coarse grained modeling of RNA Free Genesilico
YASARA Yes Yes Yes Yes No No Yes No Yes No Yes No Interactive simulations Proprietary www.YASARA.org

See also

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References

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