Download Monte Carlo, Adaptive Integration and Protein

Monte Carlo, Adaptive Integration and Protein-Protein Interactions
Authors: Christopher A. Mirabzadeh, F. Marty Ytreberg
Background and Objective:
Our objective is to develop more efficient methods for calculating protein-protein binding
affinities and using them to understand protein evolution. Specifically, we are developing the
Adaptive Integration Method for use in larger simulation packages such as GROMACS
Molecular Dynamics Simulation package.
Methods:
Alchemical Free Energy Molecular Dynamics Simulations
Results:
There are several free energy methods for molecular systems. The Adaptive Integration method
promises to provide high quality, precise, rapid estimates of binding free energies.
Discussion and Conclusions:
Binding affinity is critical for understanding protein-protein interactions and allows prediction of
changes in interaction due to evolution.
Affiliations:
University of Idaho
Collaboratorium for Modeling Complex Interactions