Comparison of nucleic acid simulation software
Appearance
This is a list of computer programs that are used for nucleic acids simulations.
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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[dead link] 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[dead link] 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
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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. and 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.
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: CS1 maint: multiple names: authors list (link) - ^ 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.
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: Unknown parameter|lastauthoramp=
ignored (|name-list-style=
suggested) (help) - ^ 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.
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: 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: 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.
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suggested) (help) - ^ Petr Šulc, Flavio Romano, Thomas E. Ouldridge, Lorenzo Rovigatti, Jonathan P. K. Doye and Ard A. Louis (2012). "Sequence-dependent thermodynamics of a coarse-grained DNA model". J. Chem. Phys.: 135101. doi:10.1063/1.4754132.
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: CS1 maint: multiple names: authors list (link)