MOE is not a software package in the usual sense, but an integrated Methodology Development Platform; that is, a tool for chemical computing software development and deployment. MOE integrates visualization, simulation and application development in one package. Custom methodology modules can be developed with the built-in high-performance data-parallel programming language SVL, the Scientific Vector Language.

MOE delivers the following benefits:

• Time Savings. SVL programs are concise and easy to write. Reductions in code size of 10 to 1 are routinely realized. Because SVL programs are small and portable (running on any platform that MOE runs on), maintenance costs are minimized as well.

• Creative Throughput. New methodology can be prototyped, experimented with, modified and verified quickly. In almost all cases, no recoding to C or Fortran is necessary since SVL is a high-performance programming language.

• Research Competitiveness. With C or Fortran, the incorporation of the latest theoretical ideas requires significant resources. Often, the costs are prohibitive and scientists are forced to wait until commercial versions become available. With MOE, the latest published methodology can be implemented and validated with minimal expenditure.

• Cost Savings. A significant amount of commercial computational chemistry software can be implemented with MOE with extremely few lines of code. The MOE system provides the critical mass of tools needed to reduce the dependence on software that integrates poorly with in-house methodology.

The following is a schematic of the architecture of MOE.

1. SVL Methodology, Libraries, Applications

Using MOE's built-in high-performance programming language, SVL, new chemical computing methodology can be implemented quickly and easily. >From rapid methodology prototyping and validation to application deployment, MOE dramatically increases a computational chemist's productivity and research throughput.

The Scientific Vector Language (SVL), is a new high-performance data-parallel programming language built into the MOE Molecular Operating Environment. SVL is an embedded language; that is, its compiler and run-time environment are an integral part of MOE. SVL serves as the command, macro, scripting, and high-performance computing language of MOE.

Standard and add-on SVL applications from Chemical Computing Group provide the starting point for as-is applications use or custom SVL methodology development. The base MOE system comes with the source code for many SVL programs.

2. Graphical User Interface Toolkit

The Graphical User Interface Toolkit facilities of SVL make interface design and implementation fast and painless. Powerful and automatic control panel layout algorithms, a rich set of high-level interface widgets, bubble help facilities and the multi-thread paradigm are the gateway to fast interface development.

For example, a Molecular Mechanics energy minimization interface that looks like: complete with Bubble Help (or Tool Tips) and data value validation requires roughly fifty lines of SVL code.

3. Molecular Tools

The heart of MOE's chemical awareness is the collection of flexible and powerful molecular data structures and algorithms. These facilities can be exploited through the use of SVL, the built-in programming language of MOE. The generic molecular tools of MOE contain:

• Hierachical object-oriented molecular data structures.
• Flexible and extensible energy models.
• Substructure search facilities.
• Random-access read/write molecular databases.
• Automatic bond order and RS chirality detection.
• Protein construction and analysis facilities.

4. Portability Toolbox

The MOE system delivers two layers of portability.

Firstly, SVL, the built-in programming language of MOE, is a byte-code layer of portability in that SVL programs will run on all machines to which MOE has been ported.

Secondly, the internal MOE architecture has a portability layer that isolates all operating and window system specific code. With only 4000 lines of machine specific code, MOE is truly portable.

Our goal is to have every SVL program automatically parallelized. This means a single SVL source program would be used for both sequential and parallel computers.

Chemical Computing Group Inc. is pleased to make its chemical computing software, MOE - the Molecular Operating Environment, more available to members of the academic community. We will be providing academic researchers MOE's full range of capabilities and functionality, but at a greatly discounted pricing schedule.

MOE delivers academic researchers:

• A customizable environment allowing for quick prototyping of new ideas and the ability to create your own end applications;
• A unique teaching tool that allows your students to "look under the hood" at the underlying algorithms;
• Out-of-the-box functionality covering the spectrum of drug research delivering powerful ready-to-use applications in the areas of: HTS, Combichem, protein/homology modeling, modeling & simulations and methods development.

Chemical Computing Group is pleased to announce that the latest version of its web page contains a "guest feature" by Dr. Jeffry Madura from Dusquesne University entitled: "Experiences Using MOE in Academia."

This feature explores how one university is using MOE to further research and education in 5 different areas: Docking, Poisson-Boltzmann Electrostatics, Gaussian Molecular Orbitals, Dynamics Animation, and in the Classroom. Samples of Dr. Madura's uses and experiences in each area are included in the article.

MOE can aid in your research through its:

• Built in applications, source code for easy customization and an embedded programming language for quick prototyping of new ideas.
• Full integration of visualization and simulation of proteins and small molecules.
• Platform independence: running on WIN 95-98, NT, SGI UNIX/NT, SUN, DEC Alpha NT, and HP-UX.
• Variety of Access Modes from graphical to batch and new to MOE WEB MODE ACCESS!
• Turn key package that includes applications in the areas of HTS, Combichem, Protein Modeling and 3D Bioinformatics, Molecular Modeling and Simulation and Methods Development.

Pam Newton