Upcoming Events

This online talk by Antonija Kuzmanic from Schrodinger will cover protein-ligand structures and drug design along with her experiences developing a career in industry.

Registration: free, but required - click here!

Title: Application of molecular dynamics simulations in predicting and analysing protein-ligand interactions

Abstract: Many structure-based drug design (SBDD) methods, including advanced free energy calculations, require accurate, atomic-level detail of the target protein structure in complex with a member of the ligand series of interest to perform optimally. Consequently, the domain of applicability of SBDD is limited by the availability of high-resolution crystal structures of the target protein or its close homologues. Alternatively, low-resolution structures could also be of use, but they might need refining, while AlphaFold2 structures completely lack a bound ligand, so the subtle details of protein-ligand interactions are left undetermined. In this talk, I will discuss simulation-based approaches that allow us to elucidate the intricacies of the protein-ligand interactions with a focus on a recently developed workflow (IFD-MD) that can predict the atomic details of the protein-ligand complex structure needed for SBDD, starting from either the target with a different ligand in the binding site or from a structure of a highly homologous protein.