Medicinal Chemistry Applications

MOE is the ideal system for large scale deployment of molecular modeling and cheminformatics applications to occasional users such as medicinal chemists. MOE has the advantage of having a flexible and customizable interface. MOE applications are easy to use and workflow or customized tools can be added. MOE is ported to a wide variety of computer platforms including Intel computers running Microsoft Windows™, Mac OS and Mac OS X.

MOE/web: Web Browser Applications MOE/web is an application environment that allows for large scale deployment of MOE applications or custom SVL programs to occasional users such as medicinal chemists via a simple web interface. MOE/web is distributed with MOE and customized applications can be incorporated.

A 2D active site analysis tool to easily identify polar, hydrophobic, acidic and basic residues. Visualize solvent exposed ligand atoms and residues in close contact with ligand atoms as well as sidechain and backbone acceptor and donor interactions. Browse through a chemical series in 2D with fixed receptor and visualize conserved and unconserved interactions for selectivity analysis.

An integrated application for active site analysis and visualization. Build Molecular Surfaces colored by atomic properties, predict Contact Preferences using statistical knowledge-based potentials and calculate Electrostatic Maps using the non-linear Poisson-Boltzmann equation. Identify steric limits, regions for ligand modification and understand receptor recognition preferences.

A streamlined interface for interactive 3D ligand optimization in the active site. A dedicated button bar provides commands for structure preparation, active site analysis, molecular property/binding affinity calculations and ligand modification and optimization in the active site. LigX can be used by both computational and medicinal chemists.

Use Link pharmacophore annotations for scaffold replacement or mimetic projects. Link annotations denote substitution points on a candidate scaffold molecule and the locations of potential R-group substituents. Search standard 3D databases or special scaffold and linker databases to find novel chemical scaffolds that preserve substituents geometry. Add additional pharmacophore features to preserve known scaffold interactions or volume constraints to satisfy shape requirements.

Multiple Molecule Flexible Alignment Performs a 3D alignment (or superposition) of known and putative ligands to deduce structural requirements for biological activity. This is especially useful if detailed structural information of a receptor is not available. MOE uses an all-atom flexible alignment procedure that combines a forcefield and a 3D similarity function based upon Gaussian descriptions of shape and pharmacophore features to produce an ensemble of possible alignments of a collection of small molecules.

Conformation Generation, Analysis, & Clustering Perform a conformational analysis using a Molecular Dynamics, Stochastic or Systematic search methodology (with full choice of forcefield). Use a fragment-based High Throughput methodology for construction of large conformation databases. Visualize and analyze the resulting ensembles of conformations in the MOE database viewer.