Current State-of-the-art for Virtual Screening and Docking Methods - New Developments in Medicinal Chemistry - page 105

CONSENSUS-DOCK is a customized version of the Dock4 program in which
three scoring functions (DOCK4, FlexX and PMF) and consensus scoring have
been implemented [542].
MOE multidisciplinary integrated platform and available source code provides
flexibility to a wide range of scientific researchers. It is an all-in-one molecular
modeling and visualization tool that is easily integrated and customizable. Users
can add new functionality or make changes to existing algorithms. It contains a
suite of pharmacophore discovery applications used for fragment-, ligand- and
structure-based design projects. Pharmacophore modeling generates and use 3D
information to search for novel active compounds, particularly when no receptor
geometry is available using a generalized molecular recognition representation
and geometric constraints to bypass the structural or chemical class bias of 2D
methods. Ligand- and Structure-Based Query Editor Construct queries with an
easy-to-use interactive query editor using either proteins or ligands (which can
screen a conformational database to determine candidate active compounds that
satisfy the pharmacophore model). It can customize pharmacophore annotations
with SMARTS chemical patterns and Boolean expressions. It can also restrict
shape (receptor or ligand) with volume constraints and refine the query with
directional vector constraints, centroids of atoms, or partial matches on
annotations. Active site analyses tools help identify key interactions of molecular
recognition. Automatic Pharmacophore Generation and induced molecular
alignments (from a collection of input compounds (possibly with activity data)).
All possible discrete geometries and all possible combinations of feature query
expressions are considered, enforcing limits on feature counts. Score queries are
based on known active compound coverage, statistical activity enrichment and
atomic overlap of matching conformations. Protein Ligand Interaction
Fingerprints also automatically generated from bound ligands given a set of
aligned complexes (or docking results). It rapidly screens a conformational
database for compound conformations that satisfy a pharmacophore query. It
searches multiple databases, a sub-range of molecules or a database of docked
compounds. Partial matches, SMARTS patterns, output of all symmetric matches
and specification of essential features are supported [543-545].