Comparison of nucleic acid simulation software

This is a list of 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	No	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
HyperChem	Yes	Yes	Yes	Yes	Yes	No	Yes	No	Yes	Yes	Yes	No	some force fields	Proprietary	Hypercube, Inc.
ICM^[2]	Yes	Yes	Yes	No	Yes	No	No	Yes	No	Yes	No	No	Global optimization	Proprietary	Molsoft
JUMNA^[3]	No	Yes	Yes	No	No	No	No	Yes	No	Yes	No	No		Proprietary
MDynaMix^[4]	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)^[5]	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^[6]	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
YASARA	Yes	Yes	Yes	Yes	No	No	Yes	No	Yes	No	Yes	No	Interactive simulations	Proprietary	www.YASARA.org

References

↑ Cornell W.D.; Cieplak P.; Bayly C.I.; Gould I.R.; Merz K.M., Jr.; Ferguson D.M.; Spellmeyer D.C.; Fox T.; Caldwell J.W.; Kollman P.A. (1995). "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules". J. Am. Chem. Soc. 117: 5179–5197. doi:10.1021/ja00124a002.
↑ Abagyan R.A., Totrov M.M. & Kuznetsov D.A. (1994). "Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation". J. Comp. Chem. 15: 488–506. doi:10.1002/jcc.540150503.
↑ Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comp. Phys. Commun. 91: 135–158. Bibcode:1995CoPhC..91..135L. doi:10.1016/0010-4655(95)00046-I.
↑ A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128: 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9.
↑ Macke T. & Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
↑ Petr Šulc; Flavio Romano; Thomas E. Ouldridge; Lorenzo Rovigatti; Jonathan P. K. Doye; Ard A. Louis (2012). "Sequence-dependent thermodynamics of a coarse-grained DNA model". J. Chem. Phys.: 135101. arXiv:1207.3391. Bibcode:2012JChPh.137m5101S. doi:10.1063/1.4754132.

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