List 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 - Ligands interactions. HA - Hardware accelerated.

Name	View 3D	Model Build	Min	MD	MC	REM	Crt	Int	Exp	Imp	Lig	HA	Comments	License	Homepage
Abalone	+	+	+	+	+	+	+		+	+	+	+	DNA, proteins, ligands	Free	Agile Molecule
AMBER [1]		+	+	+		+	+		+	+	+		AMBER Force Field	Commercial	ambermd.org
Ascalaph Designer	+	+	+	+			+		+	+	+		AMBER	GPL	biomolecular-modeling.com
CHARMM		+	+	+	+		+		+	+	+		CHARMM Force Field	Commercial	charmm.org
ICM[2]	+	+	+		+			+		+			Global optimization	Commercial	Molsoft
JUMNA [3]		+	+					+		+				Commercial
MDynaMix [4]	+	+		+			+		+		+		Common MD	GPL	Stockholm University
MOE	+	+	+	+			+		+		+		Molecular Operating Environment	Commercial	Chemical Computing Group
NAB [5]		+											Nucleic Acid Builder	GPL	New Jersey University
NAMD	+		+	+			+		+		+	+	NAnoscale Molecular Dynamics	Free	University of Illinois
oxDNA [6]	+	+		+	+	+	+			+		+	Coarse-grained models of DNA and RNA	GPL	dna.physics.ox.ac.uk
YASARA	+	+	+	+			+		+		+		Interactive simulations	Commercial	www.YASARA.org

See also

• Nucleic acid structure prediction
• Molecular Modelling
• Molecular modelling on GPU
• 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 gene prediction software
• List of RNA structure prediction software
• List of software for molecular mechanics modeling
• List of software for Monte Carlo molecular modeling
• List of software for nanostructures modeling
• Force field
• Force field implementation

References

1. 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.
2. Abagyan R.A., Totrov M.M. and 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.
3. 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.
4. 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.
5. Macke T. and Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
6. 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.