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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, now succeeded by the Macromolecular Crystallographic Information File, mmCIF format. 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 which has kept data on biological macromolecules in the newer Macromolecular Crystallographic Information File, PDBx/mmCIF file format since 2014. History The PDB file format was invented in 1972 as a human-readable file that would allow researchers to exchange the atomic coordinates in a given protein through a database system. Its fixed-column width format is limited to 80 or 140 columns, which was based on the width of the computer punch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, 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 organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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UGENE
UGENE is computer software for bioinformatics. It helps biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. UGENE integrates dozens of well-known biological tools, algorithms, and original tools in the context of genomics, evolutionary biology, virology, and other branches of life science. UGENE works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2. The data can be stored both locally and on shared/networked storage. The graphical user interface (GUI) provides access to pre-built tools so users with no computer programming experience can access those tools easily. UGENE also has a command-line interface to execute Workflows. Using UGENE Workflow Designer, it is possible to streamline a multi-step analysis. The workflow consists of blocks such as data r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulations to assist in solving chemical problems. It uses methods of theoretical chemistry incorporated into computer programs to calculate the structures and properties of molecules, groups of molecules, and solids. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion (dihydrogen cation), achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena. Overview Computational chemistry differs from theoretical chemistry, which involves a mathematical description of chem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the 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. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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MMDB
The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and hosted by the National Center for Biotechnology Information. See also * Protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ... References External links * https://www.ncbi.nlm.nih.gov/structure Biological databases National Institutes of Health Protein structure {{Biodatabase-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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List Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also * Car–Parrinello molecular dynamics * Comparison of force-field implementations * Comparison of nucleic acid simulation software * List of molecular graphics systems * List of protein structure prediction software * List of quantum chemistry and solid-state physics software * List of software for Monte Carlo molecular modeling * List of software for nanostructures modeling *Molecular design software *Molecular dynamics * Molecular modeling on GPUs *Molecule editor *PyMOL PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universall ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Python (programming Language)
Python is a high-level programming language, high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is type system#DYNAMIC, dynamically type-checked and garbage collection (computer science), garbage-collected. It supports multiple programming paradigms, including structured programming, structured (particularly procedural programming, procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC (programming language), ABC programming language, and he first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000. Python 3.0, released in 2008, was a major revision not completely backward-compatible with earlier versions. Python 2.7.18, released in 2020, was the last release of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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ScientificPython
SciPy (pronounced "sigh pie") is a free and open-source Python library used for scientific computing and technical computing. SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, fast Fourier transform, signal and image processing, ordinary differential equation solvers and other tasks common in science and engineering. SciPy is also a family of conferences for users and developers of these tools: SciPy (in the United States), EuroSciPy (in Europe) and SciPy.in (in India). Enthought originated the SciPy conference in the United States and continues to sponsor many of the international conferences as well as host the SciPy website. The SciPy library is currently distributed under the BSD license, and its development is sponsored and supported by an open community of developers. It is also supported by NumFOCUS, a community foundation for supporting reproducible and accessible science. Components The SciPy package is at the c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Chemical File Format
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 (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 ) * ''f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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ParaView
ParaView is an open-source multiple-platform application for interactive, scientific visualization. It has a client–server architecture to facilitate remote visualization of datasets, and generates level of detail (LOD) models to maintain interactive frame rates for large datasets. It is an application built on top of the Visualization Toolkit (VTK) libraries. ParaView is an application designed for data parallelism on shared-memory or distributed-memory multicomputers and clusters. It can also be run as a single-computer application. Summary ParaView is an open-source, multi-platform data analysis and visualization application. ParaView is known and used in many different communities to analyze and visualize scientific data sets. It can be used to build visualizations to analyze data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was develope ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Discovery Studio
Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA (formerly Accelrys). The product suite has a strong academic collaboration programme, supporting scientific research and makes use of a number of software algorithms developed originally in the scientific community, including CHARMM, MODELLER, DELPHI, ZDOCK, DMol3 and more. Scope Discovery Studio provides software applications covering the following areas: * Simulations ** Including Molecular Mechanics, Molecular Dynamics, Quantum Mechanics ** For molecular mechanics based simulations: Include implicit and explicit-based solvent models and membrane models ** Also includes the ability to perform hybrid QM/MM calculations * Ligand Design ** Including tools for enumerating molecular libraries and library optimization * Pharmacophore modeling ** Including creation, validation and virtual screening * Structure-based Desi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |