Calculation of Free Energy Reaction Network of Alanine Polypeptide by Using Free Energy Reaction Route Mapping Method
نویسندگان
چکیده
منابع مشابه
Saturation Mutagenesis by Efficient Free-Energy Calculation
Single-point mutations in proteins can greatly influence protein stability, binding affinity, protein function or its expression per se. Here, we present accurate and efficient predictions of the free energy of mutation of amino acids. We divided the complete mutational free energy into an uncharging step, which we approximate by a third-power fitting (TPF) approach, and an annihilation step, w...
متن کاملCalculation of free-energy differences and potentials of mean force by a multi-energy gap method.
A method is proposed to significantly accelerate the convergence of free-energy calculations. It introduces a bias factor in Monte Carlo simulations or, equivalently, a bias force in molecular dynamics simulations. The bias factor targets the energy gap, i.e., the difference in energy function between two states, and is therefore specifically designed for calculating free-energy differences. Th...
متن کاملDiffusive reaction dynamics on invariant free energy profiles.
A fundamental problem in the analysis of protein folding and other complex reactions in which the entropy plays an important role is the determination of the activation free energy from experimental measurements or computer simulations. This article shows how to combine minimum-cut-based free energy profiles (F(C)), obtained from equilibrium molecular dynamics simulations, with conventional his...
متن کاملA hybrid potential reaction path and free energy study of the chorismate mutase reaction.
We present a combination of two techniques--QM/MM statistical simulation methods and QM/MM internal energy minimizations--to get a deeper insight into the reaction catalyzed by the enzyme chorismate mutase. Structures, internal energies and free energies, taken from the paths of the reaction in solution and in the enzyme have been analyzed in order to estimate the relative importance of the reo...
متن کاملCalculation 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 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 Computer Chemistry, Japan
سال: 2019
ISSN: 1347-1767,1347-3824
DOI: 10.2477/jccj.2019-0045