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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.