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Comparison of nucleic acid simulation software

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From Wikipedia, the free encyclopedia

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 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

See also

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References

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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.
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