From Wikipedia, the free encyclopedia
This is a list of notable 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
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
LAMMPS CG-DNA
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
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 .