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Schrodinger Workshop June 1-3, 2015 · ISB 321 Day 1: Introduction to Structure-based Drug Design Session 1: Principles of Structure-based Drug Design Description: In this half-day workshop we will introduce concepts related to structure-based drug design. The workshop will consist of both lecture and hands-on application using tools in Schrodinger’s Small Molecule Drug Discovery Suite. Topics covered will include methods for structure preparation, small molecule library preparation, and using the Maestro graphical user interface. Session 2: Structure-based Virtual Screening Using Glide. Description: In this half-day workshop we will cover the basics of structure-based virtual screening using the program Glide. The workshop will consist of both lecture and hands-on application. During the hands on portion we will work through a real-world example, from initial steps to analysis of results. Day 2: Introduction to Cheminformatics and Ligand-based Drug Design Session 1: Introduction to Cheminformatics with Canvas Description: This workshop will consist of a short introductory lecture on cheminformatics followed by a handson tutorial using the program Canvas. Topics covered during the hands-on portion include property and fingerprint calculations, data visualization, R-group analysis, and QSAR modeling. Session 2: 3D approaches for Ligand-based Virtual Screening Description: In this workshop we will discuss three-dimensional approaches for ligand-based virtual screening, including (1) field-based QSAR, (2) shape-based screening, and (3) pharmacophore searching. The workshop will include both lecture and hands-on training. Day 3: Tools for Structural Modeling Session 1: Introduction to Homology Modeling with Prime Description: In this workshop, attendees will explore useful techniques to predict a structure for FactorXa, using 2 known templates, bovine factor Xa and human thrombin. This exercise explores the full use of PrimeHomology Modeling interface, and options for aligning and editing sequences are shown. The quality of the predicted model is assessed using Ramachandran plot and protein report tools and finally a newly predicted loop is refined using Prime Refinement. Given the retrospective nature of this example, the quality of the final refined prediction will be assesses by comparing to a known crystal structure. Session 2: Improved Antibody Modeling using BioLuminate Description: In this workshop we will explore the use of antibody modeling-related tools available through BioLuminate, Schrodinger's Pymol-like interface for biologics modeling. Topics covered include structuralmodeling, aggregation hot spot prediction, residue scanning, and affinity maturation. A short introduction to the BioLuminate interface will precede the antibody modeling portion of the training.