title: Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations.
abstract: Obtaining absolute binding free energies from unbiased ligand diffusion has attracted a significant amount of attention due to its implications in drug design. Several studies have used special purpose computers and software to achieve microsecond molecular dynamics which, combined with a Markov state model analysis, are capable of providing absolute binding free energies. We have recently developed a Monte Carlo based technique, PELE, capable of performing a dynamical exploration of the protein-ligand energy landscape including free ligand diffusion into the active site, at a fraction of the computational cost of molecular dynamics techniques. We demonstrate here the capabilities of our Monte Carlo technique in obtaining absolute binding free energies for a series of benzamidine like inhibitors into trypsin. Our results are in good agreement with experimental data and other molecular dynamics simulations, indicating that PELE can be a useful tool for quick estimates of binding free energies and mechanisms.
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Ryoji
authors.initials: R
authors.lastname: Takahashi
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Víctor A
authors.initials: VA
authors.lastname: Gil
authors.affiliation: Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys 23, 08010 Barcelona, Spain.
authors.forename: Victor
authors.initials: V
authors.lastname: Guallar