Comparison of nucleic acid simulation software
This is a list of 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 | 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
- Nucleic acid structure prediction
- Molecular Modelling
- Molecular modeling on GPUs
- Molecular graphics
- Molecular mechanics
- Molecular dynamics
- Molecular design software
- Molecule editor
- Quantum chemistry computer programs
- List of molecular graphics systems
- List of protein structure prediction software
- List of sequence alignment software
- List of gene prediction software
- List of RNA structure prediction software
- Comparison of software for molecular mechanics modeling
- List of software for Monte Carlo molecular modeling
- List of software for nanostructures modeling
- Force field
- Comparison of force field implementations
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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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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