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Molecular mechanics and dynamics of biomolecules using a solvent continuum model

✍ Scribed by F. Fogolari; G. Esposito; P. Viglino; H. Molinari

Publisher
John Wiley and Sons
Year
2001
Tongue
English
Weight
365 KB
Volume
22
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson–Boltzmann equation (polar contribution) and the solvent‐accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830–1842, 2001

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