Absolute free energies estimated by combining precalculated molecular fragment libraries.
The absolute free energy--or partition function, equivalently--of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by precalculating fragment configurations and interactions for reuse in a variety of molecules. We use such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost and are used to check our results by comparison to standard dynamics simulation. We explain how our work can be extended to estimate relative binding affinities.
Zhang
Xin
X
Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
Mamonov
Artem B
AB
Zuckerman
Daniel M
DM
D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008956:Models, Chemical; D009842:Oligopeptides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry*; D013816:Thermodynamics
D004151:Dipeptides; D009842:Oligopeptides; D011108:Polymers; C002956:alanylalanine; C026593:alanyl-alanyl-alanyl-alanine