14/12/2017

Thesis lecture of Gerard Martínez: Applications of molecular dynamics in drug discovery and technology transfer via a web-based platform

Next wednesday, 20th of December at 12h, Gerard Martínez from the Computational Biophysics group of GRIB will defense his thesis "Applications of molecular dynamics in drug discovery and technology transfer via a web-based platform" at the Ramón y Cajal room at the ground floor of the PRBB building. You are all invited to this event.

Abstract: high-throughput molecular dynamics (MD) simulation is a valuable computational tool to study protein-ligand interactions and protein conformational plasticity at an atomic resolution. In this doctoral thesis we applied it to drug discovery by (1) running the first MD-driven 150-fragment screening against the chemokine CXCL12 with a total simulation time of 8.2ms, (2) developing an application to detect cryptic binding sites based on simulations of protein in a mixed solution of water/benzene and (3) studying the molecular basis of functional selectivity by simulating the μ-opioid receptor bound to two different ligands for 500 μs. Additionally, we have developed a web platform called PlayMolecule where we shared with the scientific community some of the applications developed during this thesis, including a tool for protein preparation before running molecular simulations.