A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.
Cheminformatics refers to use of physical chemistry theory with computer and information science techniques—so called "in silico" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such in silico techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied.
Chemical Markup Language is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on an XML Schema, the most robust and widely used system for precise information management in many areas. It has been developed over more than a decade by Murray-Rust, Rzepa and others and has been tested in many areas and on a variety of machines.
This article discusses some common molecular file formats, including usage and converting between them.
Chemical table file is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms.
Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. Ghemical relies on external code to provide the quantum-mechanical calculations — MOPAC provides the semi-empirical MNDO, MINDO, AM1, and PM3 methods, and MPQC methods based on Hartree–Fock calculations.
OpenEye Scientific Software is an American software company which develops large-scale molecular modelling applications and toolkits.
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0.
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna.
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.
This page describes mining for molecules. Since molecules may be represented by molecular graphs this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances. One way to do this is chemical similarity metrics, which has a long tradition in the field of cheminformatics.
Peter Murray-Rust is a chemist currently working at the University of Cambridge. As well as his work in chemistry, Murray-Rust is also known for his support of open access and open data. However, he has also been criticised by Jeffrey Beall for his views on predatory publishers and especially his involvement with publisher MDPI.
BALL is software consisting of the versatile C++ class framework Biochemical Algorithms Library (BALL), a set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
ChemAxon is a cheminformatics and bioinformatics software development company specializing in cloud based, end user solutions, back end platforms and consultancy services for chemical and biological research. Headquartered in Budapest, Hungary with 121 employees. The company also operates business and consultancy offices in Cambridge, MA, San Diego, CA, and in Prague. ChemAxon has distributors in China, India, Japan, South Korea, Singapore, and Australia. ChemAxon provides solutions, platforms, applications, and consultancy services for handling chemical and biological entities for the pharmaceutical, biotechnology, new materials, fine-, petro- and agrochemical, food and cosmetics industries. ChemAxon supports academic institutions through special software licensing programs for students, teachers, academic researchers, and high school curriculums. Tools and software solutions are offered to academic research groups wishing to integrate cheminformatic functionalities into open website platforms via web hosting services.
Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obelisk, among which, in alphabetical order, Avogadro, Bioclipse, cclib, Chemistry Development Kit, GaussSum, JChemPaint, JOELib, Kalzium, Openbabel, OpenSMILES, and UsefulChem.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
Christoph Steinbeck is a chemist born in Neuwied in 1966 and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia, Germany.
Cheminformatics toolkits are software development kits that allow cheminformaticians to develop custom computer applications for use in virtual screening, chemical database mining, and structure-activity studies. Toolkits are often used for experimentation with new methodologies. Their most important functions deal with the manipulation of chemical structures and comparisons between structures. Programmatic access is provided to properties of individual bonds and atoms.
The hierarchical editing language for macromolecules (HELM) is a method of describing complex biological molecules. It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers.
