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 YesYesYesYesYesYesYesNoYesYesYesYesDNA, proteins, ligandsFreeAgile Molecule
AMBER[1] NoYesYesYesNoYesYesNoYesYesYesYes[2]AMBER force fieldProprietaryambermd.org
Ascalaph Designer YesYesYesYesNoNoYesNoYesYesYesNoAMBERFree, GPLbiomolecular-modeling.com
CHARMM NoYesYesYesYesNoYesNoYesYesYesNoCHARMM force fieldProprietarycharmm.org
CP2K NoNoYesYesYesYesYesNoYesNoNoYesFree, GPLcp2k.org
Forecaster (Fitted)[3] YesNoYesNoNoNoYesNoYesNoYesNoSmall molecule docking to nucleic acids with water placementFree for academia, ProprietaryMolecular Forecaster Archived 2019-07-09 at the Wayback Machine
ICM[4] YesYesYesNoYesNoNoYesNoYesNoNoGlobal optimizationProprietaryMolsoft
JUMNA[5] NoYesYesNoNoNoNoYesNoYesNoNoProprietary
MDynaMix[6] YesYesNoYesNoNoYesNoYesNoYesNoCommon MDFree, GPLStockholm University
Molecular Operating Environment (MOE) YesYesYesYesNoNoYesNoYesNoYesNoProprietaryChemical Computing Group
Nucleic Acid Builder (NAB)[7] NoYesNoNoNoNoNoNoNoNoNoNoGenerates models for unusual DNA, RNAFree, GPLNew Jersey University
NAnoscale Molecular Dynamics (NAMD) YesNoYesYesNoNoYesNoYesNoYesYesFast, parallel MD, CUDAFreeUniversity of Illinois
oxDNA[8][9] YesYesYesYesYesYesYesNoNoYesNoYesCoarse-grained models of DNA, RNAFree, GPLdna.physics.ox.ac.uk

LAMMPS CG-DNA

QRNAS [10] NoNoYesNoNoNoYesNoNoYesNoNoHigh resolution refinement of models of RNA, DNA and hybrids using AMBER force field .Free, GPLGenesilico Github
SimRNA[11] YesYesNoNoYesYesYesYesNoYesNoNoCoarse grained modeling of RNAFree for Academic, ProprietaryGenesilico
SimRNAweb[12] YesYesNoNoYesYesYesYesNoYesNoNoCoarse grained modeling of RNAFreeGenesilico
YASARA YesYesYesYesNoNoYesNoYesNoYesNoInteractive simulationsProprietarywww.YASARA.org

See also

References

  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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