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Comparison of nucleic acid simulation software

{{short description|None}}

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

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class="wikitable sortable"
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}}[http://www.biomolecular-modeling.com/Abalone/ Agile Molecule]
AMBER{{cite journal |

doi=10.1021/ja00124a002 |author1=Cornell W.D. |author2=Cieplak P. |author3=Bayly C.I. |author4=Gould I.R. |author5=Merz K.M., Jr. |author6=Ferguson D.M. |author7=Spellmeyer D.C. |author8=Fox T. |author9=Caldwell J.W. |author10=Kollman P.A. |

title=A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules |

journal= J. Am. Chem. Soc. |volume=117 |issue=19 |pages=5179–5197 |year=1995|citeseerx=10.1.1.323.4450 }}

| {{no}}

{{yes}}{{yes}}{{yes}}{{no}}{{yes}}{{yes}}{{no}}{{yes}}{{yes}}{{yes}}{{yes}}{{Cite web|url=http://ambermd.org/GPUSupport.php|title=The pmemd.cuda GPU Implementation}}AMBER force field{{proprietary}}[http://ambermd.org ambermd.org]
Ascalaph Designer

| {{yes}}

{{yes}}{{yes}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{yes}}{{yes}}{{no}}AMBER{{free}}, GPL[http://www.biomolecular-modeling.com/Ascalaph/Ascalaph_Designer.html biomolecular-modeling.com]
CHARMM

| {{no}}

{{yes}}{{yes}}{{yes}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{yes}}{{yes}}{{no}}CHARMM force field{{proprietary}}[https://web.archive.org/web/20090325101042/http://www.charmm.org/ charmm.org]
CP2K

| {{no}}

{{no}}{{yes}}{{yes}}{{yes}}{{yes}}{{yes}}{{no}}{{yes}}{{no}}{{no}}{{yes}}{{free}}, GPL[http://www.cp2k.org/ cp2k.org]
Forecaster (Fitted){{cite journal |last1=Wei |first1=Wanlei |last2=Luo |first2=Jiaying |last3=Waldispühl |first3=Jérôme |last4=Moitessier |first4=Nicolas |title=Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes |journal=Journal of Chemical Information and Modeling |date=24 June 2019 |volume=59 |issue=6 |pages=2941–2951 |doi=10.1021/acs.jcim.9b00163 |pmid=30998377 |s2cid=121630416 |issn=1549-960X|url=https://escholarship.mcgill.ca/concern/articles/4q77fx02n }}

| {{yes}}

{{no}}{{yes}}{{no}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{no}}Small molecule docking to nucleic acids with water placementFree for academia, Proprietary[https://www.molecularforecaster.com/products#drug-discovery-anchor Molecular Forecaster] {{Webarchive|url=https://web.archive.org/web/20190709153812/https://www.molecularforecaster.com/products#drug-discovery-anchor |date=2019-07-09 }}
ICM{{cite journal |

doi=10.1002/jcc.540150503 |author1=Abagyan R.A., Totrov M.M. |author2=Kuznetsov D.A. |name-list-style=amp|

title=Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation |

journal=J. Comput. Chem. |volume=15 |issue=5 |pages=488–506 |year=1994|s2cid=206038130 }}

| {{yes}}

{{yes}}{{yes}}{{no}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{no}}Global optimization{{proprietary}}[http://www.molsoft.com Molsoft]
JUMNA{{cite journal |

doi=10.1016/0010-4655(95)00046-I |

author=Lavery, R., Zakrzewska, K. and Sklenar, H. |

title=JUMNA: junction minimisation of nucleic acids |

journal= Comput. Phys. Commun. |volume=91 |

issue=1–3 |pages=135–158 |year=1995 |bibcode= 1995CoPhC..91..135L}}

| {{no}}

{{yes}}{{yes}}{{no}}{{no}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{no}}{{proprietary}}
MDynaMix{{cite journal |

doi= 10.1016/S0010-4655(99)00529-9 |

title= MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures |

author= A.P.Lyubartsev, A.Laaksonen |

journal= Computer Physics Communications |volume= 128 |

issue= 3 |year=2000 |pages= 565–589 |bibcode= 2000CoPhC.128..565L}}

| {{yes}}

{{yes}}{{no}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{no}}Common MD{{free}}, GPL[http://www.fos.su.se/~sasha/mdynamix/ Stockholm University]
Molecular Operating Environment (MOE)

| {{yes}}

{{yes}}{{yes}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{proprietary}}[http://www.chemcomp.com/ Chemical Computing Group]
Nucleic Acid Builder (NAB){{cite journal |author1=Macke T. |author2=Case D.A. |name-list-style=amp|

title= Modeling unusual nucleic acid structures |

journal= Molecular Modeling of Nucleic Acids |

pages=379–393 |year=1998}}

| {{no}}

{{yes}}{{no}}{{no}}{{no}}{{no}}{{no}}{{no}}{{no}}{{no}}{{no}}{{no}}Generates models for unusual DNA, RNA{{free}}, GPL[http://casegroup.rutgers.edu New Jersey University]
NAnoscale Molecular Dynamics (NAMD)

| {{yes}}

{{no}}{{yes}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{yes}}Fast, parallel MD, CUDA{{free}}[http://www.ks.uiuc.edu/Research/namd/ University of Illinois]
oxDNA{{cite journal |

doi= 10.1063/1.4754132 |pmid=23039613 |author1=Petr Šulc |author2=Flavio Romano |author3=Thomas E. Ouldridge |author4=Lorenzo Rovigatti |author5=Jonathan P. K. Doye |author6=Ard A. Louis |

title= Sequence-dependent thermodynamics of a coarse-grained DNA model |

journal= J. Chem. Phys. |volume=137 |issue=13 |

pages=135101 |year=2012|arxiv=1207.3391 |bibcode=2012JChPh.137m5101S |s2cid=15555697 }}{{cite journal |

doi=10.1140/epje/i2018-11669-8 | pmid=29748779 | author1=Oliver Henrich | author2=Yair Augusto Gutiérrez Fosado | author3=Tine Curk | author4=Thomas E Ouldridge |

title= Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications |

journal = Eur. Phys. J. E | volume=41 | issue=5 | pages=57 | year=2018 | arxiv=1802.07145| s2cid=3431325 }}

| {{yes}}

{{yes}}{{yes}}{{yes}}{{yes}}{{yes}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}Coarse-grained models of DNA, RNA{{free}}, GPL[http://dna.physics.ox.ac.uk dna.physics.ox.ac.uk]

[https://docs.lammps.org/Packages_details.html#pkg-cg-dna LAMMPS CG-DNA]

QRNAS {{Cite journal|last1=Stasiewicz|first1=Juliusz|last2=Mukherjee|first2=Sunandan|last3=Nithin|first3=Chandran|last4=Bujnicki|first4=Janusz M.|date=2019-03-21|title=QRNAS: software tool for refinement of nucleic acid structures|journal=BMC Structural Biology|volume=19|issue=1|pages=5|doi=10.1186/s12900-019-0103-1|pmid=30898165|issn=1472-6807|pmc=6429776 |doi-access=free }}

| {{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[http://genesilico.pl/software/stand-alone/qrnas Genesilico] [https://github.com/sunandanmukherjee/QRNAS.git Github]
SimRNA{{Cite journal|last1=Boniecki|first1=Michal J.|last2=Lach|first2=Grzegorz|last3=Dawson|first3=Wayne K.|last4=Tomala|first4=Konrad|last5=Lukasz|first5=Pawel|last6=Soltysinski|first6=Tomasz|last7=Rother|first7=Kristian M.|last8=Bujnicki|first8=Janusz M.|date=2015-12-19|title=SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction|journal=Nucleic Acids Research|volume=44|issue=7|pages=e63|doi=10.1093/nar/gkv1479|pmid=26687716|issn=0305-1048|pmc=4838351}}

| {{yes}}

{{yes}}{{No}}{{No}}{{Yes}}{{Yes}}{{Yes}}{{Yes}}{{No}}{{Yes}}{{No}}{{No}}Coarse grained modeling of RNAFree for Academic, Proprietary[http://genesilico.pl/software/stand-alone/simrna Genesilico]
SimRNAweb{{Cite journal|last1=Magnus|first1=Marcin|last2=Boniecki|first2=Michał J.|last3=Dawson|first3=Wayne|last4=Bujnicki|first4=Janusz M.|date=2016-04-19|title=SimRNAweb: a web server for RNA 3D structure modeling with optional restraints|journal=Nucleic Acids Research|volume=44|issue=W1|pages=W315–W319|doi=10.1093/nar/gkw279|pmid=27095203|pmc=4987879|issn=0305-1048}}

| {{yes}}

{{yes}}{{No}}{{No}}{{Yes}}{{Yes}}{{Yes}}{{Yes}}{{No}}{{Yes}}{{No}}{{No}}Coarse grained modeling of RNA|Free[https://genesilico.pl/SimRNAweb/ Genesilico]
YASARA

| {{yes}}

{{yes}}{{yes}}{{yes}}{{no}}{{no}}{{yes}}{{no}}{{yes}}{{no}}{{yes}}{{no}}Interactive simulations{{proprietary}}[http://www.yasara.org www.YASARA.org]

See also

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References

{{Reflist}}

{{DEFAULTSORT:Nucleic acid simulation software}}

Category:Computational chemistry software

Category:Software comparisons

Category:Molecular dynamics software

Category:Molecular modelling software

{{Computer simulation}}