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.


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. DeschĂȘnes 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 P. Labute
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 and Analysis P. Labute
An Integrated Application in MOE for the Visualization and Analysis of Protein Active Sites with Molecular Surfaces, Contact Statistics and Electrostatic Maps.


2D Structure Depiction A. M. Clark
Structure diagrams can be generated from molecular connection tables in MOE.


Molecular Orbitals in MOE A. M. Clark
New functionality in MOE for plotting molecular orbitals generated from MOPAC wavefunctions.

Relational Database Access in MOE S. Burlington
An overview of the JDBC model used in MOE for connecting to and manipulating relational databases.

Overview of Pharmacophore Applications in MOE A. Lin
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 M. Soss
Using MOE's protein consensus and contact applications, the structurally conserved core of a family of kinases is examined.

Rotamer Exploration and Prediction M. Soss
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 MOE 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 Compound Libraries N. Flanagan
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 K. Kelly
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 Protein Structures 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 coordinates.

Probabilistic Receptor Potentials P. Labute
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 distributions.

A Widely Applicable Set of Descriptors P. Labute
A collection of 32 new molecular descriptors are presented for use in QSAR/QSPR, cheminformatics and HTS QSAR applications.

QuaSAR-Descriptor A. Lin
An overview of the collection of molecular descriptors in MOE is presented.

Experiences Using MOE in Academia Jeffry D. Madura
Five different areas in which MOE is used to further research and education in the Department of Chemistry & Biochemistry at Duquesne University.

3D Bioinformatics and Comparative Modeling in MOE K. Kelly
Overview of the MOE protein tools and presentation of CASP results.

Molecular Databases and MOE 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 efficient.

Flexible Alignment of Small Molecules P. Labute
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 analysis.

Exhaustive and Iterative Clustering of the Protein Databank K. Kelly
Improved homology identification and modeling is obtained by multiple-sequence and structural alignments computed from experimental structures.

Molecular Builders S. Murray
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 P. Labute
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 A. Lin
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 and surfaces.

The P's and Q's of Methodology Development P. Labute
Methodology development and code portability are key issues for industrial discovery-based research companies. Ensuring the supply of new methodology will be of critical importance.

SVL: The Scientific Vector Language 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.

Graphical Interface Programming in MOE D. Labute
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 QSAR/QSPR A. Lin
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 D. Labute
Prompting for molecular objects is an important tool for interactive SVL programs in the MOE environment. This article is dedicated to interface development.

Protein Structure Validation and Analysis K. Kelly
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 P. Labute
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 deployment techniques.

Multiple Sequence and Structure Alignment in MOE K. Kelly
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 Interface Toolkit D. Labute
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 P. Moser
Overview of some of MOE's applications and tools for polymer property prediction.

The C Application Programming Interface to SVL M. Santavy
Although most MOE programming is done in the SVL programming language, a language extension system is provided that allows SVL access to C code libraries.

The MOE Crystal Builder A. Lin
Description of the MOE Crystal Builder along with examples of its use.

Protein Analysis in MOE: The Serine Proteases K. Kelly
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 P. Labute
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 P. Labute
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 Order P. Labute
The algorithm used in MOE for the automatic assignment of bond order is described.

The MOE Nonlinear Optimization Library P. Labute
The nonlinear optimization tools of MOE are among the most powerful known. In particular, the Truncated Newton method delivers superlinear convergence rates yet requires little memory.

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.

MOE Forcefield Facilities P. Labute
The forcefield facilities of MOE allow for a wide range of current forcefield parameters and atom types to be specified.

Programming With SVL Vectors M. Santavy
A tutorial on vector-based programming in SVL using Coulomb's law as an example.