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

Major New Features in MOE 2011.10

	Non-Bonded Interaction Visualization Model	Sequence Editor Redesign
	Combinatorial Build in Pocket	Analysis of Solvent in Binding
	Macromolecular System Preparation	GPCR Family Database and Alignment Tools

Major New Features in PSILO 2011.09

3D searches for protein-ligand and protein-protein interactions Faster pocket similarity searching Automatic protein kinase annotation

User Group Meeting 2012

North American UGM & Conference June 26 - 29, 2012 Montreal, Canada

Journal Articles

Scaffold Replacement in MOE S. Grimshaw A new application for performing scaffold replacements, fragment linking, and R-group optimization is presented. The application is applied to the discovery of novel p38 MAP kinase inhibitors, using the structures of a screening hit and the mature BIRB-796 inhibitor as starting points.

Training a Scoring Function for the Alignment of Small Molecules S. L. Chan and P. Labute A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed. J Chem Inf Model, 2010, 50 (9), pp 1724-1735

Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors W. F. Long and P. Labute A set of physicochemical properties describing a protein of known structure is employed for a calibrative approach to protein solubility. J Comput Aided Mol Des, 2010

Pocket Similarity: Are α Carbons Enough? H. J. Feldman and P. Labute A novel method for measuring protein pocket similarity was devised, using only the α carbon positions of the pocket residues. J Chem Inf Model, 2010, 50 (8), pp 1466-1475

LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops P. Labute We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. J Chem Inf Model, 2010, 50 (5), pp 792-800