Phase , Schrödinger's software for pharmacophore modeling and ligand-based drug design, has been the subject of ambitious and ongoing development since its initial 1.0 release in early 2005. In this seminar, product manager Steve Dixon discusses newly available features in Phase 2.5, with a special emphasis on shape-based searching. Dr. Dixon will cover the methodology for Phase's new shape-based searching tool, and review preliminary results obtained with it.

The presentation will last about one hour, and includes time for a question-and-answer session.

KNIME has established itself as the leading open-source data pipelining tool, and provides an ideal platform for researchers looking for a way to combine best-of-breed technologies, both commercial and academic. Schrödinger KNIME Extensions provide nearly 100 "nodes" for researchers needing to rapidly develop, validate, and deploy molecular modeling and cheminformatics workflows, as well as pre-assembled, editable workflows that use Schrödinger nodes. In this seminar, Schrödinger Director of Applications Science Woody Sherman provides an overview of Schrödinger KNIME Extensions, and explains how to create workflows using the KNIME interface.

The presentation will last about one hour, and includes time for a question-and-answer session.

Fragment-based docking is an excellent approach to structure-based drug design when novel chemotypes are required. In this seminar, Woody Sherman, Schrödinger's Director of Applications Science, describes recent work using pharmacophore models derived from fragment docking experiments. Topics covered include the use of Glide XP to accurately place fragments, the use of a modified ligand binding efficiency to discern active from inactive fragments, the creation of pharmacophore hypotheses using docked and rank-ordered fragments, and successful database screens performed using these hypotheses.

The presentation will last about one hour, and includes time for a question-and-answer session.

Maestro , Schrödinger's molecular visualization environment and graphical user interface, is regularly used to create high-quality images for publication. In this seminar, Schrödinger Media Director Mike Campbell provides an overview of how to save publication- and presentation-quality images with Maestro, and describes how to use Maestro's visualization and rendering settings for maximum effect when creating images to accompany published research.

The presentation will last about one hour, and includes time for a question-and-answer session.

Schrödinger has developed its Induced Fit Docking methodology to accurately predict ligand binding modes in circumstances where changes to the receptor shape are needed to accommodate the ligand. The method involves a combination of Glide docking using a softened potential, followed by a Prime

protein structure refinement, and finishes with a Glide energy evaluation to obtain the top-scoring ligand-receptor pair. Validation studies have been performed on targets for which standard docking methods fail, and show that Induced Fit Docking can be successfully applied to a wide variety of relevant targets.

The presentation will last about one hour, and includes time for a question-and-answer session.

From importing raw crystallographic data to exporting a refined, all-atom protein structure, PrimeX provides a complete toolbox for crystallographers while still allowing for easy import and export of intermediate structures for use with third-party programs. Building upon Prime , Schrödinger's well-received software for protein structure prediction, the newly available PrimeX is unique in its use of an all-atom force field and incorporation of highly regarded loop- and sidechain-prediction tools. In this seminar, PrimeX product manager Jeff Bell discusses the design and use of PrimeX, as well as the rationale behind PrimeX's use of an all-atom force field. Describing common errors in crystallographic structures that are easily resolved with an all-atom force field, as well as the benefits of creating an all-atom structure that's less likely to be modified by downstream users, Dr. Bell will present material on both technical and practical issues.

The presentation will last about one hour, and includes time for a question-and-answer session.