Comparison of nucleic acid simulation software
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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 | 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 |
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
- 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
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