Generates energy minimized 3D molecular structures. LigPrep can correct Lewis structures by applying sophisticated rules. It eliminates mistakes in ligands to reduce downstream computational errors. The tool provides filters that permit to eliminate compounds that do not meet user-specified criteria in order to generate a completely customized ligand library. It processes fast to permit the conversion of entire databases at one time.
Aims at highlighting pharmacophore information from known and unknown protein-ligand complexes. LigandScout is an algorithm that extracts, in an automated way, ligands including interpretation and identification of the relevant amino acids. This method intends to increase the efficiency of the interpretation of ligand topology by the generation of pharmacophore models.
Generates bioactive conformers of drug-like molecules. ConfGen is based on the infrastructure from the general molecular modeling program MacroModel. It allows access to multiple all-atom force fields, redundant conformer elimination, and multiple processor computing. The tool offers features to limit the number of ring system conformations sampled, including an upper limit, a maximum number of the lowest energy ring conformations per ring system to use and a maximum overall number of ring conformations.
Automates docking jobs with AutoDock. DOVIS is a utility software and a Linux cluster-based application that can reliably screen millions of compounds against a receptor and automatically save the top percentage of high-scoring hits. It runs in parallel on hundreds of central processing units (CPUs) and docks large numbers (millions) of ligands to a target receptor. It also automatically partitions input ligands, prepares parameter files for AutoDock, launches parallel AutoDock runs, parses results, and saves a set of top-ranking docked ligands.
An integrated drug discovery software. MOE is able to track design ideas and ligand modifications with property models, produce correlation plots to visualize Structure, Property, Activity Relationships and visualize hydrophobic and charged protein surface to study aggregation prone regions. It can also automatically align and superpose antibody structures using the MOE Project protocol, generate and search advanced antibody queries with the Project Search application and build full length Ig structures including bispecifics with the Antibody Homology Modeler.
Accounts for receptor flexibility in ligand-receptor docking by iteratively combining rigid receptor docking with protein structure prediction and refinement. Induced Fit generates viable receptor ensembles that can be used in virtual database screens. This tool allows to produce viable receptor structures that, as part of an ensemble with other conformations of the receptor, can produce significantly higher enrichment factors in database screening.
Offers a cost-effective way to identify and order new drug candidates has been recently launched. mcule provides a comprehensive, carefully curated database of molecules immediately available for virtual screening. It provides a convenient, online solution for managing compound databases and libraries as molecule collections. The user can keep track on all the previous compound selections and get back to start the compound ordering process whenever it is necessary.