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.

More information Name, View 3D ...
Name View 3D Model build Min MD MC REM Crt Int Exp Imp Lig GPU Comments License Website
Abalone YesYesYesYesYesYesYesNoYesYesYesYesDNA, proteins, ligandsFreeAgile Molecule
AMBER[1] NoYesYesYesNoYesYesNoYesYesYesYes[2]AMBER force fieldProprietaryambermd.org
Ascalaph Designer YesYesYesYesNoNoYesNoYesYesYesNoAMBERFree, GPLbiomolecular-modeling.com
CHARMM NoYesYesYesYesNoYesNoYesYesYesNoCHARMM force fieldProprietarycharmm.org
CP2K NoNoYesYesYesYesYesNoYesNoNoYesFree, GPLcp2k.org
Forecaster (Fitted)[3] YesNoYesNoNoNoYesNoYesNoYesNoSmall molecule docking to nucleic acids with water placementFree for academia, ProprietaryMolecular Forecaster Archived 2019-07-09 at the Wayback Machine
ICM[4] YesYesYesNoYesNoNoYesNoYesNoNoGlobal optimizationProprietaryMolsoft
JUMNA[5] NoYesYesNoNoNoNoYesNoYesNoNoProprietary
MDynaMix[6] YesYesNoYesNoNoYesNoYesNoYesNoCommon MDFree, GPLStockholm University
Molecular Operating Environment (MOE) YesYesYesYesNoNoYesNoYesNoYesNoProprietaryChemical Computing Group
Nucleic Acid Builder (NAB)[7] NoYesNoNoNoNoNoNoNoNoNoNoGenerates models for unusual DNA, RNAFree, GPLNew Jersey University
NAnoscale Molecular Dynamics (NAMD) YesNoYesYesNoNoYesNoYesNoYesYesFast, parallel MD, CUDAFreeUniversity of Illinois
oxDNA[8][9] YesYesYesYesYesYesYesNoNoYesNoYesCoarse-grained models of DNA, RNAFree, GPLdna.physics.ox.ac.uk

LAMMPS CG-DNA

QRNAS [10] NoNoYesNoNoNoYesNoNoYesNoNoHigh resolution refinement of models of RNA, DNA and hybrids using AMBER force field .Free, GPLGenesilico Github
SimRNA[11] YesYesNoNoYesYesYesYesNoYesNoNoCoarse grained modeling of RNAFree for Academic, ProprietaryGenesilico
SimRNAweb[12] YesYesNoNoYesYesYesYesNoYesNoNoCoarse grained modeling of RNAFreeGenesilico
YASARA YesYesYesYesNoNoYesNoYesNoYesNoInteractive simulationsProprietarywww.YASARA.org
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References

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