Dia is free and open source general-purpose diagramming software, developed originally by Alexander Larsson. It uses a controlled single document interface (SDI) similar to GIMP and Inkscape.
Scalable Vector Graphics (SVG) is an XML-based vector image format for defining two-dimensional graphics, having support for interactivity and animation. The SVG specification is an open standard developed by the World Wide Web Consortium since 1999.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). These structural data are obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organisations.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
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.
A molecule editor is a computer program for creating and modifying representations of chemical structures.
A chemical file format is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the chemical table file format, which is similar to Structure Data Format (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another.
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.
A number of vector graphics editors exist for various platforms. Potential users of these editors will make a comparison of vector graphics editors based on factors such as the availability for the user's platform, the software license, the feature set, the merits of the user interface (UI) and the focus of the program. Some programs are more suitable for artistic work while others are better for technical drawings. Another important factor is the application's support of various vector and bitmap image formats for import and export.
An image file format is a file format for a digital image. There are many formats that can be used, such as JPEG, PNG, and GIF. Most formats up until 2022 were for storing 2D images, not 3D ones. The data stored in an image file format may be compressed or uncompressed. If the data is compressed, it may be done so using lossy compression or lossless compression. For graphic design applications, vector formats are often used. Some image file formats support transparency.
This article describes the technical specifications of the OpenDocument office document standard, as developed by the OASIS industry consortium. A variety of organizations developed the standard publicly and make it publicly accessible, meaning it can be implemented by anyone without restriction. The OpenDocument format aims to provide an open alternative to proprietary document formats.
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.
JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other operating systems supporting the programming language Java. It is free and open-source software distributed under the GNU General Public License (GPL) 2.0.
MDL Information Systems, Inc. was a provider of R&D informatics products for the life sciences and chemicals industries. The company was launched as a computer-aided drug design firm in January 1978 in Hayward, California. The company was acquired by Symyx Technologies, Inc. in 2007. Subsequently Accelrys merged with Symyx. The Accelrys name was retained for the combined company. In 2014 Accelrys was acquired by Dassault Systemes. The Accelrys business unit was renamed BIOVIA.
ISIS/Draw was a chemical structure drawing program developed by MDL Information Systems. It introduced a number of file formats for the storage of chemical information that have become industry standards.
ChemDraw is a molecule editor first developed in 1985 by Selena "Sally" Evans, her husband David A. Evans, and Stewart Rubenstein. The company was sold to PerkinElmer in 2011. ChemDraw, along with Chem3D and ChemFinder, is part of the ChemOffice suite of programs and is available for Macintosh and Microsoft Windows.
A nuclear magnetic resonance spectra database is an electronic repository of information concerning Nuclear magnetic resonance (NMR) spectra. Such repositories can be downloaded as self-contained data sets or used online. The form in which the data is stored varies, ranging from line lists that can be graphically displayed to raw free induction decay (FID) data. Data is usually annotated in a way that correlates the spectral data with the related molecular structure.
