منابع مشابه
Protein Force Fields
Proteins are arguably the most chemically, structurally, and functionally diverse of the biologically relevant macromolecules. In biological systems, amino acids, the smallest common subunit of proteins, function as intermediates for a variety of biosynthetic pathways, can be diverted for use as sources of energy, and function as neurotransmitters. Polypeptides, containing from two to approxima...
متن کاملPolarizable force fields.
Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water--or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics o...
متن کاملOptimizations of protein force fields
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various methods for force-field parameter optimizations. Finally, some examples of our applications of these parameter optimization methods are given and they are compared...
متن کاملReactive force fields made simple.
Generating a reactive force field for a given chemical reaction is turned from a many-months project for experts into a task of a few hours for a non-specialist, by joining the newly developed quantum-mechanically derived force field (QMDFF) and Warshel's time-tested empirical valence bond (EVB) idea. Three first example applications demonstrate that this works not just for simple atom exchange...
متن کاملDynamic properties of force fields.
Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated wi...
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ژورنال
عنوان ژورنال: Wiley Interdisciplinary Reviews: Computational Molecular Science
سال: 2011
ISSN: 1759-0876
DOI: 10.1002/wcms.89