Comparison of nucleic acid simulation software explained

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															Agile Molecule
AMBER^[1]												^[2]			ambermd.org
Ascalaph Designer															biomolecular-modeling.com
CHARMM															charmm.org
CP2K															cp2k.org
Forecaster (Fitted)^[3]													Small molecule docking to nucleic acids with water placement		Molecular Forecaster
ICM^[4]															Molsoft
JUMNA^[5]
MDynaMix^[6]													Common MD		Stockholm University
Molecular Operating Environment (MOE)															Chemical Computing Group
Nucleic Acid Builder (NAB)^[7]													Generates models for unusual DNA, RNA		New Jersey University
NAnoscale Molecular Dynamics (NAMD)													Fast, parallel MD, CUDA		University of Illinois
oxDNA^[8] ^[9]													Coarse-grained models of DNA, RNA		dna.physics.ox.ac.ukLAMMPS CG-DNA
QRNAS ^[10]													High resolution refinement of models of RNA, DNA and hybrids using AMBER force field .		Genesilico Github
SimRNA^[11]													Coarse grained modeling of RNA	Free for Academic, Proprietary	Genesilico
SimRNAweb^[12]													Coarse grained modeling of RNA		Free	Genesilico
YASARA													Interactive simulations		www.YASARA.org
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Notes and References

1. 10.1021/ja00124a002 . 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. . A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules . J. Am. Chem. Soc. . 117 . 19 . 5179–5197 . 1995. 10.1.1.323.4450 .
2. Web site: The pmemd.cuda GPU Implementation.
3. Wei . Wanlei . Luo . Jiaying . Waldispühl . Jérôme . Moitessier . Nicolas . Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes . Journal of Chemical Information and Modeling . 24 June 2019 . 59 . 6 . 2941–2951 . 10.1021/acs.jcim.9b00163 . 30998377 . 121630416 . 1549-960X.
4. 10.1002/jcc.540150503 . Abagyan R.A., Totrov M.M. . Kuznetsov D.A. . amp. Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation . J. Comput. Chem. . 15 . 5 . 488–506 . 1994. 206038130 .
5. 10.1016/0010-4655(95)00046-I . Lavery, R., Zakrzewska, K. and Sklenar, H. . JUMNA: junction minimisation of nucleic acids . Comput. Phys. Commun. . 91 . 1–3 . 135–158 . 1995 . 1995CoPhC..91..135L.
6. 10.1016/S0010-4655(99)00529-9 . MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures . A.P.Lyubartsev, A.Laaksonen . Computer Physics Communications . 128 . 3 . 2000 . 565–589 . 2000CoPhC.128..565L.
7. Macke T. . Case D.A. . amp. Modeling unusual nucleic acid structures . Molecular Modeling of Nucleic Acids . 379–393 . 1998.
8. 10.1063/1.4754132 . 23039613 . Petr Šulc . Flavio Romano . Thomas E. Ouldridge . Lorenzo Rovigatti . Jonathan P. K. Doye . Ard A. Louis . Sequence-dependent thermodynamics of a coarse-grained DNA model . J. Chem. Phys. . 137 . 13 . 135101 . 2012. 1207.3391 . 2012JChPh.137m5101S . 15555697 .
9. 10.1140/epje/i2018-11669-8 . 29748779 . Oliver Henrich . Yair Augusto Gutiérrez Fosado . Tine Curk . Thomas E Ouldridge . Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications . Eur. Phys. J. E . 41 . 5 . 57 . 2018 . 1802.07145. 3431325 .
10. Stasiewicz. Juliusz. Mukherjee. Sunandan. Nithin. Chandran. Bujnicki. Janusz M.. 2019-03-21. QRNAS: software tool for refinement of nucleic acid structures. BMC Structural Biology. 19. 1. 5. 10.1186/s12900-019-0103-1. 30898165. 1472-6807. 6429776 . free .
11. Boniecki. Michal J.. Lach. Grzegorz. Dawson. Wayne K.. Tomala. Konrad. Lukasz. Pawel. Soltysinski. Tomasz. Rother. Kristian M.. Bujnicki. Janusz M.. 2015-12-19. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Research. 44. 7. e63. 10.1093/nar/gkv1479. 26687716. 0305-1048. 4838351.
12. Magnus. Marcin. Boniecki. Michał J.. Dawson. Wayne. Bujnicki. Janusz M.. 2016-04-19. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic Acids Research. 44. W1. W315–W319. 10.1093/nar/gkw279. 27095203. 4987879. 0305-1048.