Wednesday, October 6

Schrödinger Applications Scientists and research scientists from D.E. Shaw Research are holding hands-on workshops as detailed below. Participants will perform hands-on activities in Maestro and will also learn how to automate workflows using KNIME, guided by the Associate Product Manager for KNIME extensions Jean-Christophe Mozziconacci.

13:00 - 14:15
Advanced MD using Desmond
István Kolossváry and John Klepeis, D.E. Shaw Research

This hands-on workshop will include setting up Desmond simulations with Windows Maestro for protein and membrane systems as well as a replica exchange simulation. Participants will be provided with whole trajectories for Maestro and VMD based analysis. Participants are encouraged to bring their own systems in a Maestro file for customized Desmond setup. The
Desmond Tutorial document and a set of workshop slides will also be provided.

14:15 - 15:30
Conformational analysis in various degree of accuracy
David Rinaldo, Schrödinger

Exploration of conformational space is one of the main issues in structure and ligand-based methods. In this workshop we will review different methods available from the Schrodinger Suite to generate conformations and also how to analyze your results. Examples of conformational generation and analysis
will be taken from various methods including Molecular Dynamics and Quantum Calculations.

15:30 - 16:00 Coffee Break

16:00 - 17:15
HTVS: What do I do with the hit list?
Daniel Cappel, Schrödinger

This is an FXa virtual screening study using 1F0R and known FXa inhibitors. We start by using SiteMap to explore the active and site and examine self-docking results. We then practice how to use an automated Virtual Screening Workflow, looking at the set-up in detail, and follow through with different tools which allow us to post-process the results. These include MM-GBSA, constraint-filters, clustering methods, structural interaction fingerprints (SIFt) as well as pharmacophore hypotheses. We will also look at fragment-based exploration of the pocket. Additionally, we will see how you can use a shape-based method as a prefilter.

17:15 - 18:30
Turn your chemical data inside-out
Jianxin Duan, Schrödinger

Canvas will be used to explore a series of CI tasks which could represent a typical workflow in a Biotech Company.  We will start with how to analyze, query, filter, and import data into a compound database. We will then use assorted methods to identify similar compounds using reference ligands. Finally, we will analyze HTS results to find common substructures with which we will query the database. The query and screening results will be compiled with a view to purchasing them from a minimum common supplier.