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 DNA, proteins, ligands Agile Molecule AMBER AMBER force field ambermd.org Ascalaph Designer AMBER , GPL biomolecular-modeling.com CHARMM CHARMM force field charmm.org CP2K , GPL cp2k.org Forecaster (Fitted) Small molecule docking to nucleic acids with water placement Free for academia, Proprietary Molecular Forecaster ICM Global optimization Molsoft JUMNA MDynaMix Common MD , GPL Stockholm University Molecular Operating Environment (MOE) Chemical Computing Group Nucleic Acid Builder (NAB) Generates models for unusual DNA, RNA , GPL New Jersey University NAnoscale Molecular Dynamics (NAMD) Fast, parallel MD, CUDA University of Illinois oxDNA Coarse-grained models of DNA, RNA , GPL dna.physics.ox.ac.uk LAMMPS CG-DNAQRNAS High resolution refinement of models of RNA, DNA and hybrids using AMBER force field . , GPL Genesilico GithubSimRNA Coarse grained modeling of RNA Free for Academic, Proprietary Genesilico SimRNAweb Coarse grained modeling of RNA Free Genesilico YASARA Interactive simulations www.YASARA.org
See also
References