Canvas is powerful set of tools for ligand-based drug discovery, and has been well-received by experienced cheminformatics researchers who have been using early versions of the program from the command line. In this presentation, Canvas Product Manager Dr. Steve Dixon delivers an overview of the Canvas graphical user interface (GUI) that will be released as part of Schrodinger Suite 2009. The Canvas GUI is designed to be an intuitive interface to the program's many robust computational tools, and is well-equipped to handle the extremely large ligand libraries that characterize cheminformatics research.

In this seminar, Applications Scientist Dr. Kathryn Loving provides an overview of Schrodinger tools geared toward fragment-based lead generation, lead optimization, and pharmacophore generation. These tools utilize a range of 3D structural information to perform fragment docking, joining, linking, and clustering. Additionally, Dr. Loving will present Schrodinger's implementation of structure interaction fingerprints and show how these fingerprint profiles can be used to analyze and optimize fragment screening results. The seminar will also address challenges associated with fragment-based design.

Jaguar, used for fast ab initio calculations, and MacroModel, used for general modeling, can be used to answer a wide variety of basic research questions. In this presentation, Schrodinger Media Director Mike Campbell presents an overview of how to use the Maestro interface to run both Jaguar and MacroModel calculations, refine MacroModel results using Jaguar, and view results.

Maestro affords users access to its internal workings by way of Python bindings that allow user-created scripts to call common functions. In turn, this allows custom Python scripts to be rapidly developed for specific purposes, as developers need not write excess code that unnecessarily duplicates Maestro functionality. In this presentation, Vice President of Applications Science Dr. Woody Sherman presents an overview of the Schrodinger Script center. The Script Center is a centralized repository for a wide variety of tools that Schrodinger has developed either in response to customer requests or in the course of our own research. Dr. Sherman will present various useful scripts including tools for automation, cheminformatics, docking and post-precessing, and other modeling tasks. Dr. Sherman will also present a selection of custom interfaces developed using Schrodinger's Python scripting tools.

Structure-based methods have great potential for predicting sites of oxidation by specific isoforms of cytochrome P450(CYP). However, there are two primary factors that hinder the success of traditional rigid-receptor docking approaches: (a) sites of oxidation do not correlate well with the most stable binding mode of a substrate, and (b) in order to accommodate structurally diverse substrates, CYP active sites are highly flexible. In this seminar, Schrodinger Applications Scientist Dr. Mee Shelley describes a new method for predicting sites of oxidation based on analysis of ensembles of structures generated by Induced Fit Docking combined with empirically derived rules that define the intrinsic reactivity of a given site. The method is highly successful in predicting sites of oxidation for a dataset of known CYP2D6 substrates.