Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space - Quantitative Biology > Quantitative MethodsReport as inadecuate




Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space - Quantitative Biology > Quantitative Methods - Download this document for free, or read online. Document in PDF available to download.

Abstract: Pre-calculated libraries of molecular fragment configurations have previouslybeen used as a basis for both equilibrium sampling via -library-based MonteCarlo- and for obtaining absolute free energies using a polymer-growthformalism. Here, we combine the two approaches to extend the size of systemsfor which free energies can be calculated. We study a series of all-atompoly-alanine systems in a simple dielectric -solvent- and find that precisefree energies can be obtained rapidly. For instance, for 12 residues, less thanan hour of single-processor is required. The combined approach is formallyequivalent to the -annealed importance sampling- algorithm; instead ofannealing by decreasing temperature, however, interactions among fragments aregradually added as the molecule is -grown.- We discuss implications for futurebinding affinity calculations in which a ligand is grown into a binding site.



Author: Steven Lettieri, Artem B. Mamonov, Daniel M. Zuckerman

Source: https://arxiv.org/







Related documents