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JSmol
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. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways. For example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a wide range of chemical file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Streptavidin
Streptavidin is a 66.0 (tetramer) kDa protein purified from the bacterium '' Streptomyces avidinii''. Streptavidin homo-tetramers have an extraordinarily high affinity for biotin (also known as vitamin B7 or vitamin H). With a dissociation constant (Kd) on the order of ≈10−14 mol/L, the binding of biotin to streptavidin is one of the strongest non-covalent interactions known in nature. Streptavidin is used extensively in molecular biology and bionanotechnology due to the streptavidin-biotin complex's resistance to organic solvents, denaturants (e.g. guanidinium chloride), detergents (e.g. SDS, Triton X-100), proteolytic enzymes, and extremes of temperature and pH. Structure The crystal structure of streptavidin with biotin bound was reported by two groups in 1989. The structure was solved using multi wavelength anomalous diffraction by Hendrickson et al. at Columbia University and using multiple isomorphous replacement by Weber et al. at E. I. DuPont Central Resea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Unix
Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others. Initially intended for use inside the Bell System, AT&T licensed Unix to outside parties in the late 1970s, leading to a variety of both academic and commercial Unix variants from vendors including University of California, Berkeley ( BSD), Microsoft ( Xenix), Sun Microsystems ( SunOS/ Solaris), HP/ HPE ( HP-UX), and IBM ( AIX). In the early 1990s, AT&T sold its rights in Unix to Novell, which then sold the UNIX trademark to The Open Group, an industry consortium founded in 1996. The Open Group allows the use of the mark for certified operating systems that comply with the Single UNIX Specification (SUS). Unix systems are characterized by a modular design that is sometimes called the " Unix philosophy". According to thi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaScript
JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of websites use JavaScript on the client side for webpage behavior, often incorporating third-party libraries. All major web browsers have a dedicated JavaScript engine to execute the code on users' devices. JavaScript is a high-level, often just-in-time compiled language that conforms to the ECMAScript standard. It has dynamic typing, prototype-based object-orientation, and first-class functions. It is multi-paradigm, supporting event-driven, functional, and imperative programming styles. It has application programming interfaces (APIs) for working with text, dates, regular expressions, standard data structures, and the Document Object Model (DOM). The ECMAScript standard does not include any input/output (I/O), such as networking, storage, or graphics facilities. In practice, the web bro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Markup Language
Chemical Markup Language (ChemML or CML) 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. Chemical information is traditionally stored in many different file types which inhibit reuse of the documents. CML uses XML's portability to help CML developers and chemists design interoperable documents. There are a number of tools that can generate, process and view CML documents. Publishers can distribute chemistry within XML documents by using CML, e.g. in RSS documents. CML is capable of supporting a wide range of chemical concepts including: * molecules * reactions * spectra and analytical data * comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MDL Molfile
Chemical table file (CT 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. File formats There are several file formats in the family. The formats were created by MDL Information Systems (MDL), which was acquired by Symyx Technologies then merged with Accelrys Corp., and now called BIOVIA, a subsidiary of Dassault Systemes of Dassault Group. CT File is an open format, BIOVIA publishes its specification. BIOVIA requires users to register to download the CTFile format specifications. Molfile An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information. The molfil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallographic Information File
Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. The file format was initially published by Hall, Allen, and Brown and has since been revised, most recently versions 1.1 and 2.0. Full specifications for the format are available at the IUCr website. Many computer programs for molecular viewing are compatible with this format, including Jmol. Closely related is mmCIF, macromolecular CIF, which is intended as an alternative to the Protein Data Bank (PDB) format. It is now the default format used by the Protein Data Bank. Also closely related is Crystallographic Information Framework, a broader system of exchange protocols based on data dictionaries and relational rule ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank (file Format)
The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cr ... which now keeps data on biological macromolecules in the newer mmCIF file format. History The PDB file format was invented in 1976 as a human-readable file that would allow researchers to exchange protein coordinates through a database system. Its fixed-column width format ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical File Format
A chemical file format is a type of data file which is used specifically to 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 (or atomic numbers) 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. Distinguishing formats Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:(see ) * ''fil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribbon Diagram
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the adjacent image. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon. Ribbon diagrams are simple yet powerful, expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Space-filling Model
In chemistry, a space-filling model, also known as a ''calotte model'', is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the distances between the atomic nuclei, all in the same scale. Atoms of different chemical elements are usually represented by spheres of different colors. Space-filling calotte models are also referred to as CPK models after the chemists Robert Corey, Linus Pauling, and Walter Koltun, who over a span of time developed the modeling concept into a useful form. They are distinguished from other 3D representations, such as the ball-and-stick and skeletal models, by the use of the "full size" space-filling spheres for the atoms. The models are tactile and manually rotatable. They are useful for visualizing the effective shape and relative dimensions of a molecule, and (because of the rotatability) t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ball-and-stick Model
In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods which represent the bonds. Double and triple bonds are usually represented by two or three curved rods, respectively, or alternately by correctly positioned sticks for the sigma and pi bonds. In a good model, the angles between the rods should be the same as the angles between the bonds, and the distances between the centers of the spheres should be proportional to the distances between the corresponding atomic nuclei. The chemical element of each atom is often indicated by the sphere's color. In a ball-and-stick model, the radius of the spheres is usually much smaller than the rod lengths, in order to provide a clearer view of the atoms and bonds throughout the model. As a consequence, the model does not provide a clear insight about t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache Taverna
Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name ''Taverna Workbench'', then a project under the Apache incubator. Taverna allowed users to integrate many different software components, including WSDL SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench. Taverna Workbench provided a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow engine was also available separately, as a Java API, command line tool or as a server. Taverna was used by users in many domains, such as bioinformatics, cheminformatics, medicine, astronomy, social science, music, and digital preservation. S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
