Comparison of nucleic acid simulation software

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DNA-(A)80-model.png

This is a list of 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 Download-Link
AMBER[1] No Yes Yes Yes No Yes Yes No Yes Yes Yes No 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 Download-Links
CHARMM No Yes Yes Yes Yes No Yes No Yes Yes Yes No CHARMM force field Proprietary charmm.org
ICM[2] Yes Yes Yes No Yes No No Yes No Yes No No Global optimization Proprietary Molsoft
JUMNA[3] No Yes Yes No No No No Yes No Yes No No Proprietary
MDynaMix[4] 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)[5] 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[6] Yes Yes No Yes Yes Yes Yes No No Yes No Yes Coarse-grained models of DNA, RNA Free, GPL dna.physics.ox.ac.uk
YASARA Yes Yes Yes Yes No No Yes No Yes No Yes No Interactive simulations Proprietary www.YASARA.org

See also[edit]

References[edit]

  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: 5179–5197. doi:10.1021/ja00124a002. 
  2. ^ 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. Comp. Chem. 15: 488–506. doi:10.1002/jcc.540150503. 
  3. ^ Lavery, R., Zakrzewska, K. and Sklenar, H. (1995). "JUMNA: junction minimisation of nucleic acids". Comp. Phys. Commun. 91: 135–158. Bibcode:1995CoPhC..91..135L. doi:10.1016/0010-4655(95)00046-I. 
  4. ^ A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128: 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9. 
  5. ^ Macke T. & Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393. 
  6. ^ 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.: 135101. doi:10.1063/1.4754132.