Application Index

Programs which do not fit into other categories. When enough programs of a similar type have fallen into the miscellaneous category, we will consider creating a new category for them.

CODESSA is an advanced, fully featured quantitative structure/activity relationship (QSAR) program that ties information from AMPAC with experimental data.
View Application Entry for CODESSA

CONCORD sets the industry standard for extremely rapid conversion of 2D (or even crude 3D) input to accurate, geometry-optimized 3D structures. CONCORD is most often used for the conversion of large corporate and commercial databases; however, CONCORD is also a computational tool that is useful for molecular modeling and QSAR/QSPR research. A part of industry and academia since 1987, CONCORD proven reliability and versatility have made it the choice of hundreds of pharmaceutical and agrochemical scientists worldwide. New enhancements with PowerCONCORD offer all the advantages of CONCORD plus parallel and distributed processing capabilities for unprecedented speed (more than half a million structures an hour, for example).
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DISCO rapidly generates multiple pharmacophore hypotheses for a given set of active compounds. Using fast computing techniques and a method of clique detection developed by Dr. Yvonne Martin and co-workers at Abbott Laboratories, DISCO identifies common pharmacophoric features in each structure, produces optimally aligned structures, and extracts the key features of the pharmacophore. These pharmacophore hypotheses can then be compared, refined, and used to guide lead generation and lead optimization.
View Application Entry for DISCO (DIStance COmparison)

DIVA is a desktop application for working with chemical and biological data.
View Application Entry for DIVA

JChemPaint is an editor for 2D Molecular Structures and is an open source program. JChemPaint, currently in release 1.1, supports a subset of the regular drawing features of commercial programs, Loading and saving of structures in Chemical Markup Language (CML), Automated Structure Layout, also known as Structure Diagram Generation, Loading structures from the Internet usign CAS or NSC number, Rudimentary Carbon NMR chemical shift range prediction based on one-sphere HOSE codes, saving bitmap and vector graphics images .
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The Molecular Operating Environment, a new generation of chemical computing software designed around a high-performance language, Scientific Vector Language. Contains built-in applications covering high throughput discovery (HTS data analysis and combinatorial chemistry); protein & homology modeling (complete sequence to structure); modeling and simulation, and corporate deployment and methods development. Source code is supplied with most of the built-in applications, users are able to customize the applications to meet their changing needs. MOE is platform independent running native on HP UX & NT, SGI, Sun, WinNT, Win95-2000, and Linux. The combination of platform independence, broad range of application areas, and flexible customization makes MOE ideals for corporate deployment. Serving: academic, pharmaceutical, biotech, combinatorial chemistry, and materials and polymer sciences.
View Application Entry for MOE (Molecular Operating Environment)

Molconn-Z is the standard program for generation of Molecular Connectivity, Shape, and Information Indices for Quantitative Structure Activity Relationship (QSAR) Analyses.
View Application Entry for Molconn-Z (Molecular Connectivity)

MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces. This program is written using the C programing language and can be used as a standalone program or as an AVS (Advanced Visualisation System) module. It has shown to be very reliable and produces very regular triangulations. Binary versions of MSMS are available for SGI, Dec Alpha, HP9000, IBM PC, Sun workstations and others.
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SIMS is a program written to calculate the molecular surface which envelops the solvent-excluded volume of the solute molecule. The calculation is based on the Connolly method which has been substantionally improved to overcome deficiencies of the Connolly method to provide a Smooth (i.e., non-singular) Invariant (i.e., independent on orientation of the molecule) Molecular Surface, The SIMS calculates a DOT presentation of the molecular surface, i.e. array of 3D coordinates of surface elements, their normal vectors and areas. Yury Vorobjev and Jan Hermans. Biophysical J. 73:722-732, 1997.
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Sysload is a simple package for monitoring the machine loads on a cluster of computers on a network. It also includes basic utilities for entering data into a database which can later be graphed for analysis etc.
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UNITY Featuring the industry-standard 3D-flexible search engine, UNITY gives you the most hits from your database in the least time-period. UNITY enables effective interrogation of multiple, distributed databases of discovery information. UNITY has been engineered for rapid data exploration and lead identification. Offering Markush-query definition, powerful links to relational databases, and integration with SYBYL and the Molecular Spreadsheet.
View Application Entry for UNITY

Usagemon is a small, simple system for tracking usage of software over a network, or for monitoring software events such as crashes, number of times a feature is used, etc. This can be useful when a developer wants to collect statistics on the reliability of a program, reporting architecture information about the machines the program is being run on (i.e. to determine what a typical configuration is) etc. Usagemon works by running a daemon on a server machine (your network somewhere) and then a small bit of code is compiled into the program(s) to be tracked, which sends a UDP packet or packets to the usage monitor with information of interest. These UDP packets are unreliable, so the data that is collected is only useful for statistical type analysis, not a guaranteed reliable count of events. It is just a mechanism with which to collect useful information.
View Application Entry for Usagemon