Other Software Links
Molecular Modeling
- Ascalaph Quantum - Ascalaph, by Agile Molecule, provides an interface for the quantum mechanical program PC GAMESS.
- Barista - BARISTA™, by Conflex, is an analysis-support platform containing functions for molecular structural analysis, molecular orbital analysis,
standard vibrational analysis, and dynamic analysis in addition to proprietary functions for multi-conformational analysis.
- BioSolveIT - Software for structure-based, ligand-based and de novo based drug design. Using these tools you can access a range of applications
that permit the design, visualization and alignment of ligand libraries, virtual screening of such ligand databases for hit identification, ligand optimization and scaffold hoping or the design of compound mimics.
- Conflex - Unique to CONFLEX, by Conflex Corp., is its capability to completely search the conformational space of a
flexible molecule to find every optimal structure of chemically significant conformers.
- Coot - Crystallographic Object-Oriented Toolkit - Coot is for model building, model completion and validation. Coot displays maps and models and
allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, etc.
- COSMOlogic - COSMOlogic is a small, but dynamic company founded in 1999 that provides software in the border region of Computational Chemistry, Physical Chemistry,
Chemical Engineering and Thermodynamics.
- Molcas - "Molcas is quantum chemistry software developed by scientists to be used by scientists."
- Molecular Evoluator - "Molecule Evoluator, by Cidrux, is a software package that aids in the development
of novel molecular templates and lead compounds.
- Materials Explorer - "Materials Explorer is a versatile engineering tool that provides
researchers with advanced modeling capabilities to investigating the structure and properties of materials at the atomic and molecular level."
- MOE - MOE, by Chemical Computing Group, is a fully integrated, drug discovery software package with tools for protein modeling and bioinformatics,
pharmacophore modeling, cheminformatics, high-throughput discovery, structure-based design, molecular modeling, and simulations and method development.
- Sirius - "Sirius is a component-based visualization framework designed for application in molecular modeling, drug discovery,
protein structure analysis, as well as database mining and sequence-based work."
- Spartan - Spartan, by Wavefunction, allows scientists to build and manipulate molecules; run molecular mechanics and
quantum chemical calculations; and analyze results with Spartan graphics, property boxes, spreadsheets, spectra, plots, and text output.
- ZMM Molecular Modeling Program - "ZMM is a molecular modeling program for the theoretical study
of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes."
Resources
- Cheminformatic Links - This website contains links to cheminformatics
programs and QSAR datasets (with structures!). All programs should be free to use, at least for academics.
- Computational Chemistry List, Ltd. - The Computational Chemistry List (CCL) was
established on January 11, 1991, as an independent electronic forum for chemistry researchers and educators from around the world.
- The QSAR and Modelling Society - The International QSAR Society was founded in 1989, at a
QSAR Gordon Conference. At the 1995 QSAR Gordon Conference, the title of the Society to The QSAR and Modelling Society.
QSAR/QSPR
- ADMEWORKS ModelBuilder - "ADMEWORKS ModelBuilder is a tool for building mathematical models that can later be used for
predicting various chemical and biological properties of compounds."
- Derek for Windows - Derek for Windows, by Lhasa Limited, is an expert knowledge base system that provides high throughput
screen for genotoxicity/mutagenicity, predictions as to whether a chemical will be a skin sensitizer or a a carcinogen, and highlights potenital toxicological
hazards covering a wide range of endpoints from irritancy to hepatotoxicity.
- Meteor - Meteor, by Lhasa Limited, is a computer program that helps scientists who need information about the
metoboloic fate of chemicals and want to be more efficient, more effective and make better decisions.
- CompuDrug - CompuDrug is a niche software corporation which has
been specializing in developing and generating ADME and drug discovery software for the past two decades.
- Net Software
- Pallas Net 2.0
- EMIL NET
- Pallas SDK 2.0
- Pallas for UNIX/Linux
- Pallas Cluster
- ADMETox
- Drug Discovery
- Lead Optimization
- Drug Disposition
- Metabolism
- Toxicity
- ProDrugs
- HPLC Analythics
- Pallas
- Plug-in
- Codessa Pro
- Sarchitect Designer - An in silico platform for building, validating, and deploying structure-activity relationship models.
Databases/Database Mining
- CambridgeSoft - CambridgeSoft's products are used primarily
in the pharmaceutical, biotechnology and chemical industries, as well as in higher education and in academic and government research.
- ChemACX
- The Merck Index
- ChemINDEX
- Ashgate Drugs
- Name=Struct
- Chemical Db
- Dotmatics Browser - Dotmatics Browser is a Web-based tool for querying, browsing, and
visualizing biological and chemical data.
- gNova Scientific Software - gNova Inc. was founded in 2005 to integrate its
newly developed database product, CHORD, with the consulting services offered through O'Donnell Associates.
- LigandScout - LigandScout, by Inte:Ligand, is a software tool that allows users to derive
3-D pharmacophores from structural data of macromolecule/ligand complexes in an automated and convenient way.
- Rational Numbers - Rational Numbers, by MathSpec, is a software application designed for identifying small
organic compounds from small organic compounds from mass spectral data.
- Vitic - Vitic, by Lhasa Limited, is a chemically intelligent toxicity database and management system
that can recognize and search for similarities in chemical structures.
Teaching Resources
- Kitechen Chemistry - An on-line course exploring the link between chemistry and the culinary arts.
- Wolfram Demostration Project - A collection of freely available, interactive Demonstrations in math, science, and many other areas - at all levels, from elementary education to front-line research
