منابع مشابه
k-Dynamics Free Energy Simulation Methods
Free energy calculations are fundamental to obtaining accurate theoretical estimates of many important biological phenomena including hydration energies, protein-ligand binding affinities and energetics of conformational changes. Unlike traditional free energy perturbation and thermodynamic integration methods, k-dynamics treats the conventional ‘‘k’’ as a dynamic variable in free energy simula...
متن کاملFree energy methods in molecular simulation
An overview is given of methods for calculating free energies by molecular simulation. Techniques may be categorized as density-of-states methods and work-based methods. Emphasis is given to the latter, with particular focus on issues of performance and accuracy. Two points of view are provided for understanding these issues. One is based on the distribution of work values observed in the calcu...
متن کاملMolecular Dynamics Simulation and Free Energy Studies on the Interaction of Salicylic Acid with Human Serum Albumin (HSA)
Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecu...
متن کاملBent surface free energy differences from simulation
We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem formula, and subsequent integration of the stress with respect to strain as a function of
متن کاملFree energy calculations by computer simulation.
A fundamental problem in chemistry and biochemistry is understanding the role of solvation in determining molecular properties. Recent advances in statistical mechanical theory and molecular dynamics methodology can be used to solve this problem with the aid of supercomputers. By using these advances the free energies of solvation of all the chemical classes of amino acid side chains, four nucl...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2009
ISSN: 0192-8651,1096-987X
DOI: 10.1002/jcc.21295