Comparison of nucleic acid simulation software

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

Min – Optimization
MD – Molecular dynamics
MC – Monte Carlo
REM – Replica exchange method
Crt – Cartesian coordinates
Int – Internal coordinates
Exp – Explicit water
Imp – Implicit water
Lig – Ligand interactions
GPU – Hardware accelerated

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

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 (19): 5179–5197. CiteSeerX 10.1.1.323.4450. doi:10.1021/ja00124a002.
"The pmemd.cuda GPU Implementation".
Wei, Wanlei; Luo, Jiaying; Waldispühl, Jérôme; Moitessier, Nicolas (24 June 2019). "Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes". Journal of Chemical Information and Modeling. 59 (6): 2941–2951. doi:10.1021/acs.jcim.9b00163. ISSN 1549-960X. PMID 30998377. S2CID 121630416.
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. Comput. Chem. 15 (5): 488–506. doi:10.1002/jcc.540150503. S2CID 206038130.
Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comput. Phys. Commun. 91 (1–3): 135–158. Bibcode:1995CoPhC..91..135L. doi:10.1016/0010-4655(95)00046-I.{{cite journal}}: CS1 maint: multiple names: authors list (link)
A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128 (3): 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. 137 (13): 135101. arXiv:1207.3391. Bibcode:2012JChPh.137m5101S. doi:10.1063/1.4754132. PMID 23039613. S2CID 15555697.
Oliver Henrich; Yair Augusto Gutiérrez Fosado; Tine Curk; Thomas E Ouldridge (2018). "Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications". Eur. Phys. J. E. 41 (5): 57. arXiv:1802.07145. doi:10.1140/epje/i2018-11669-8. PMID 29748779. S2CID 3431325.
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. doi:10.1186/s12900-019-0103-1. ISSN 1472-6807. PMC 6429776. PMID 30898165.
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. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351. PMID 26687716.
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. doi:10.1093/nar/gkw279. ISSN 0305-1048. PMC 4987879. PMID 27095203.

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[1] 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 (19): 5179–5197. CiteSeerX 10.1.1.323.4450. doi:10.1021/ja00124a002.

[2] "The pmemd.cuda GPU Implementation".

[3] Wei, Wanlei; Luo, Jiaying; Waldispühl, Jérôme; Moitessier, Nicolas (24 June 2019). "Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes". Journal of Chemical Information and Modeling. 59 (6): 2941–2951. doi:10.1021/acs.jcim.9b00163. ISSN 1549-960X. PMID 30998377. S2CID 121630416.

[4] 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. Comput. Chem. 15 (5): 488–506. doi:10.1002/jcc.540150503. S2CID 206038130.

[5] Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comput. Phys. Commun. 91 (1–3): 135–158. Bibcode:1995CoPhC..91..135L. doi:10.1016/0010-4655(95)00046-I.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[6] A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128 (3): 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9.

[7] Macke T. & Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.

[8] 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. 137 (13): 135101. arXiv:1207.3391. Bibcode:2012JChPh.137m5101S. doi:10.1063/1.4754132. PMID 23039613. S2CID 15555697.

[9] Oliver Henrich; Yair Augusto Gutiérrez Fosado; Tine Curk; Thomas E Ouldridge (2018). "Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications". Eur. Phys. J. E. 41 (5): 57. arXiv:1802.07145. doi:10.1140/epje/i2018-11669-8. PMID 29748779. S2CID 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. doi:10.1186/s12900-019-0103-1. ISSN 1472-6807. PMC 6429776. PMID 30898165.

[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. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351. PMID 26687716.

[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. doi:10.1093/nar/gkw279. ISSN 0305-1048. PMC 4987879. PMID 27095203.

Computer simulation software
Biology	Protein structure prediction Nucleic acid simulation
Chemistry	Chemical process simulators Quantum chemistry Molecular modeling Monte Carlo molecular modeling Molecular design
Physics	Finite element Cosmological simulation Dynamic simulation Dynamical simulation Electronic circuit simulation EM simulation Multiphysics simulation Reservoir simulation
Social science	Social simulation Sociology Organizational studies

Comparison of nucleic acid simulation software

See also

References