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.
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. 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Macke T. and Case D.A. (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
