Structure-Based Design Pharmacophore Discovery Protein & Antibody Modeling Molecular Modeling & Simulations Cheminformatics & (HTS) QSAR Medicinal Chemistry Applications Methods Development & Deployment

Major New Applications in MOE 2009.10

Major New Features in PSILO 2010.02

User Group Meeting 2010

European User Group Meeting October 18 - 21, 2010 Cambridge, UK

Journal Articles

2D Depiction of Fragment Hierarchies A. M. Clark A method for depicting and presenting fragment hierarchies of molecules, showing common structural features with uniform 2D depiction motifs. J. Chem. Inf. Model., 2010, 50 (1), pp 37-46

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.