Vienna Summer School on Drug Design, Vienna, Austria

September 10, 2023 to September 15, 2023

Schrödinger is excited to be participating in the Vienna Summer School on Drug Design taking place on September 10th-15th in Vienna, Austria. Join us for workshops by Zeineb Si Chaib, Senior Scientist I at Schrödinger.

Workshop 1
Structure-based drug design (SBDD): a deep dive into docking-based virtual screening
Abstract: With the recent advances in experimental techniques (CryoEM) and in predictive tools (AlphaFold2) an ever-increasing number of protein structures are becoming available. These structures can then be used to rationally design new drugs using the so-called structure-based drug discovery (SBDD) approaches. Among them, molecular docking has been very popular and is playing an important role particularly in order to find new hits by performing virtual screening of large libraries. Yet, in order to be able to use this computational method efficiently a deep understanding of the data sources and quality as far as a thorough and critical analysis of the results is essential. In this workshop, you will learn how to use Schrödinger molecular modeling technology to properly analyze and prepare the target to efficiently perform molecular docking. Then, after performing a docking-based virtual screening you will analyze your results using various techniques including filtering, clustering and diversity-based selection.
 

Workshop 2
I do not have a structure, now what?
Abstract: Many structure-based drug design (SBDD) methods, including free energy perturbation (FEP+), require accurate, atomic-level detail of the target protein in complex with a member of the ligand series being modeled to perform optimally. Experimental methods such as X-ray crystallography or cryo-electron microscopy (cryo-EM) can provide starting points for such predictions at or near an atomic level of resolution. However, the cost to experimentally obtain structures with new ligands ranges from trivial to extremely large. In this workshop, participants will learn how to properly analyze and prepare a target protein to subsequently be able to refine it using different induced-fit docking approaches, including IFD-MD. This method allows reducing time and costs, and expanding the domain of applicability of SBDD. It is an integral workflow that can predict the accurate structure of the desired ligand series starting from a structure of the target protein with a very different ligand in the binding site or even starting from a structure of a highly homologous protein, or an apo structure.

 

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