Scaffold Replacement in MOE
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.
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
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.
Ligand Interaction Diagrams
A. M. Clark
2D active site diagrams showing the ligand, nearby residues and various
types of interactions.
Active Site Visualization
An Integrated Application in MOE for the Visualization and Analysis of
Protein Active Sites with Molecular Surfaces, Contact Statistics and
2D Structure Depiction
A. M. Clark
Structure diagrams can be generated from molecular connection tables in MOE.
Molecular Orbitals in
A. M. Clark
New functionality in MOE for plotting molecular orbitals generated from MOPAC
Relational Database Access in
An overview of the JDBC model used in MOE for
connecting to and manipulating relational databases.
Overview of Pharmacophore
Applications in MOE
A look at MOE's pharmacophore applications for generating
pharmacophore queries, performing searches, and calculating
a pharmacophore consensus.
Analysis of the
Structurally Conserved Core of a Set of Proteins
Using MOE's protein consensus and contact applications,
the structurally conserved core of a family of kinases is examined.
Rotamer Exploration and
A novel approach is presented for the prediction of protein sidechain
conformations. The method is based on systematic conformational search and an
environment-based scoring function to rank the conformers.
Distributed Computing in
J. Demers, P. Labute
An overview of MOE/smp is presented. MOE/smp is an enhancement to MOE and
MOE/batch allowing multiple MOE processes to cooperate on large-scale
distributed computing tasks.
Firms Creating More Focused
A reprint from Genetic Engineering News featuring QuaSAR-Binary. It is
also available in pdf format.
Protein Structure and
Family Data in MOE 2001.01
The contents of the MOE structural family database are summarized, and
compared to the protein families and superfamilies in the SCOP. The new
capabilities of MOE's PDB reader are also summarized.
Locating Binding Sites in
P. Labute, M. Santavy
A methodology is presented for locating candidate active sites in protein
structures. The method is based upon alpha shape analysis of 3D protein
A methodology is presented for determining the preferred locations of
ligand atoms when given the 3D coordinates of a receptor. The approach is
based upon fitting experimental data with analytical probability
A Widely Applicable Set of
A collection of 32 new molecular descriptors are presented for use in
QSAR/QSPR, cheminformatics and HTS QSAR applications.
An overview of the collection of molecular descriptors in MOE is
Experiences Using MOE in
Jeffry D. Madura
Five different areas in which MOE is used to further research and
education in the Department of Chemistry & Biochemistry at Duquesne
3D Bioinformatics and
Comparative Modeling in MOE
Overview of the MOE protein tools and presentation of CASP results.
Molecular Databases and
J. Demers and S. Murray
Introduction to MOE's molecular databases, Database Viewer and sundry
database tools and applications.
Numeric Solution of the
Non-Linear Poisson-Boltzmann Equation
M. Santavy, P. Labute
A MOE application solves the non-linear Poisson-Boltzmann equation. The
results of computational experiments show the method to be accurate and
Flexible Alignment of Small
Presentation of a method for flexibly aligning a collection small
molecules. The results of several computational experiments suggest the
method's utility for the elucidation of pharmacophores and comparative field
Exhaustive and Iterative
Clustering of the Protein Databank
Improved homology identification and modeling is obtained by
multiple-sequence and structural alignments computed from experimental
MOE provides a series of desktop builders which can be used to build
small molecules, proteins, carbohydrates, as well as crystal structures.
Binary QSAR: A New
Technology for HTS and UHTS Data Analysis
High Throughput Screening promises a wealth of experimental
data. However, the large volume comes at a price. The challenge
is to extract useful information from the screening data.
X-Ray, Neutron and Electron
Diffraction Simulations in MOE
The MOE simulations suite supports X-ray, neutron and electron
diffraction simulations. Structure factors can be calculated and displayed in
a variety of formats.
Electrostatic Fields and
Surfaces in MOE
M. Santavy, P. Labute
The 1998.10 version of MOE contains some powerful new
functionality for visualizing and manipulating scalar fields
The P's and Q's of
Methodology development and code portability are key
issues for industrial discovery-based research companies.
Ensuring the supply of new methodology will be of critical
SVL: The Scientific Vector
M. Santavy, P. Labute
Unleashing the power of parallel computing devices has, in the past,
proven difficult. New high-level parallel programming languages are the
key to exploiting parallelism.
Programming in MOE
MOE provides a powerful GUI toolkit for creating graphical user interfaces
and manipulating graphical windows. The high-level approach simplifies the
task of interface programming in scientific applications.
QuaSAR: The MOE System for
Introduces the MOE system for QSAR/QSPR studies. A unique, flexible
and extensible descriptor manager is at the heart of the tool set.
Object Prompting with the
MOE Interface Toolkit
Prompting for molecular objects is an important tool for interactive
SVL programs in the MOE environment. This article is dedicated to
Validation and Analysis
Protein stereochemical validation of proposed models
is a critical step in the comparative protein modeling
process. The MOE statistical protein structure validation
tool is described in this feature.
MOE Deployment Strategies
From network browsers to desktop, workstation and compute
servers, there are many ways in which to deploy MOE and
its applications. This article surveys a number of MOE
Multiple Sequence and
Structure Alignment in MOE
Automatic multiple sequence and structural alignment
is an important component of many methodologies. This feature
presents the alignment applications in MOE.
Object Layout with the SVL
Automatic interface object layout is one of the key features
of the SVL Graphical Interface Toolkit. This article presents
the basics of window layout.
Polymer Property Prediction in MOE
Overview of some of MOE's applications and tools for polymer property
The C Application Programming
Interface to SVL
Although most MOE programming is done in the SVL programming language, a
language extension system is provided that allows SVL access to C code
The MOE Crystal Builder
Description of the MOE Crystal Builder along with examples
of its use.
Protein Analysis in MOE: The
Demonstration of the ease with which fundamental insights
can be gained into protein structure and function using
MOE's built-in suite of protein applications.
QuaSAR-Cluster: A Different
View of Molecular Clustering
A new view of the molecular clustering procedure is
presented. This method is based on multidimensional nonparametric
ranking and is applicable to very large collections.
An Efficient Algorithm for
the Determination of Topological RS Chirality
The method used in MOE for the automatic assignment
of CIP priorities to every atom in a molecule is described.
This enables correct assignment of RS chirality and is
fast enough for macromolecules.
Automatic Assignment of Bond
The algorithm used in MOE for the automatic assignment of bond order
The MOE Nonlinear Optimization
The nonlinear optimization tools of MOE are among the
most powerful known. In particular, the Truncated Newton
method delivers superlinear convergence rates yet requires
The A* Search and Applications
to Sequence Alignment
K. Kelly, P. Labute
The properties of the A* search algorithm and
applications to multiple sequence alignment are described.
The forcefield facilities of MOE allow for a wide range of current
forcefield parameters and atom types to be specified.
Programming With SVL
A tutorial on vector-based programming in SVL using Coulomb's law as an