List of nucleic acid simulation software

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DNA-(A)80-model.png

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
YASARA + + + + + + + Interactive simulations Commercial www.YASARA.org

See also[edit]

References[edit]

  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.