A | B | C | D | E | F | G | H | CH | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
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
- ^ 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.
- ^ "The pmemd.cuda GPU Implementation".
- ^ 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.
- ^ 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.
- ^ 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) - ^ 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.
- ^ 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; 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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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