Pharmacophore Discovery Structure-Based Design Protein Modeling and Bioinformatics Cheminformatics and QSAR Medicinal Chemistry Applications High Throughput Discovery Molecular Modeling and Simulations Methods Development and Deployment

New Applications and Updates in MOE 2008.10

User Group Meeting 2009

North American User Group Meeting June 23 - 26, 2009 Montreal, Canada

European User Group Meeting September 29 - October 2, 2009 Basel, Switzerland

Journal Articles

Detection and Assignment of Common Scaffolds in Project Databases of Lead Molecules A. M. Clark and P. Labute The underlying algorithms for the Structure-Activity Report are now available in the scientific literature: J. Med. Chem., 2009, 52 (2), pp 469–483

SD File Processing with MOE Pipeline Tools A. M. Clark and P. Labute We present a series of SD command line tools for the preparation of small molecule databases including protonation and tautomer enumeration, filtering, sorting and descriptor calculations.

Ligand Scaffold Replacement using MOE Pharmacophore Tools A. Deschênes and E. Sourial We describe a scaffold replacement methodology based upon an extension of MOE's pharmacophore features. The special "Link" pharmacophore features can be used in conjunction with other features, SMARTS patterns and volume constraints.

Protonate 3D: Assignment of Macromolecular Protonation State and Geometry P. Labute Protonate 3D is an application which assigns protonation states and geometries (taking titration into account) to macromolecular structures using an algorithm that solves the Unary Quadratic Optimization problem.