Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages
نویسندگان
چکیده
منابع مشابه
Free 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...
متن کاملAccuracy of free-energy perturbation calculations in molecular simulation. II. Heuristics
We examine issues involved in applying and interpreting free-energy perturbation ~FEP! calculations in molecular simulation, with the aim to develop simple heuristics that can guide their use and warn when a result is likely to be inaccurate. We build on the accuracy model developed in the first paper of this series @N. Lu and D. A. Kofke, J. Chem. Phys. 114, 7303 ~2001!#, which emphasized the ...
متن کاملAccuracy of free - energy perturbation calculations in molecular simulation . I . Modeling
We examine issues involved in applying and interpreting free-energy perturbation ~FEP! calculations in molecular simulation. We focus in particular on the accuracy of these calculations, and how the accuracy differs when the FEP is performed in one or the other direction between two systems. We argue that the commonly applied heuristic, indicating a simple average of results taken for the two d...
متن کاملPostprocessing of molecular docking poses using binding free energy calculations
The main key to success in structure-based drug discovery is the accurate prediction of binding affinities of hit compounds. Molecular docking and scoring functions are often used for this purpose. However, it is often found that the top-ranked docking poses do not represent the right binding mode, and frequently there is no correlation between docking score and biological data. Therefore, “pos...
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 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: 2018
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.8b00544