Gibbs Sampler-Based λ-Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation
نویسندگان
چکیده
منابع مشابه
Calculation of free energy changes due to mutations from alchemical free energy simulations
How a mutation a®ects the binding free energy of a ligand is a fundamental problem in molecular biology/biochemistry with many applications in pharmacology and biotechnology, e.g. design of drugs and enzymes. Free energy change due to a mutation can be determined most accurately by performing alchemical free energy calculations in molecular dynamics (MD) simulations. Here we discuss the necessa...
متن کاملNew Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodyn...
متن کاملAlchemical free energy methods for drug discovery: progress and challenges.
Improved rational drug design methods are needed to lower the cost and increase the success rate of drug discovery and development. Alchemical binding free energy calculations, one potential tool for rational design, have progressed rapidly over the past decade, but still fall short of providing robust tools for pharmaceutical engineering. Recent studies, especially on model receptor systems, h...
متن کاملGibbs sampler-based coordination of autonomous swarms
In this paper a novel, Gibbs sampler-based algorithm is proposed for coordination of autonomous swarms. The swarm is modeled as a Markov random field (MRF) on a graph with a time-varying neighborhood system determined by local interaction links. The Gibbs potential is designed to reflect global objectives and constraints. It is established that, with primarily local sensing/communications, the ...
متن کاملLinear-scaling soft-core scheme for alchemical free energy calculations
Alchemical free energy calculations involving the removal or insertion of atoms into condensed phase systems generally make use of soft-core scaling of nonbonded interactions, designed to circumvent numerical instabilities that arise from weakly interacting "hard" atoms in close proximity. Current methods model soft-core atoms by introducing a nonlinear dependence between the shape of the inter...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2017
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.7b00204