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Conformational Dynamics Data Bank
The conformational dynamics data bank (CDDB) is a database about conformational dynamics of heavy proteins and protein assemblies. The CDDB is useful when used alongside static structural data to aid research into protein function. It is also helpful in identifying protein assemblies that are essential to cell function. Analysis is carried out by coarse-grained computation of the structures present in the electron microscopy data bank The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformat ... (EMDB). This analysis shows equilibrium thermal fluctuations and elastic strain energy distributions, which allows for identification of rigid and flexible protein domains. The results also provide information on correlations in molecular motions which can be used to identify molecular regions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance. A database management system (DBMS) is the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS software additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an appli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conformational Change
In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a ''conformational change''. Factors that may induce such changes include temperature, pH, voltage, light in chromophores, concentration of ions, phosphorylation, or the binding of a ligand. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis. Laboratory analysis Many biophysical techniques such as crystallography, NMR, electron paramagnetic resonance (EPR) using spin label techniques, circular dichroism (CD), hydrogen exchange, and FRET can be used to study macrom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Immunoglobulin Heavy Chain
The immunoglobulin heavy chain (IgH) is the large polypeptide subunit of an antibody (immunoglobulin). In human genome, the IgH gene loci are on chromosome 14. A typical antibody is composed of two immunoglobulin (Ig) heavy chains and two Ig light chains. Several different types of heavy chain exist that define the class or isotype of an antibody. These heavy chain types vary between different animals. All heavy chains contain a series of immunoglobulin domains, usually with one variable domain (VH) that is important for binding antigen and several constant domains (CH1, CH2, etc.). Production of a viable heavy chain is a key step in B cell maturation. If the heavy chain is able to bind to a surrogate light chain and move to the plasma membrane, then the developing B cell can begin producing its light chain. The heavy chain doesn't always have to bind to a light chain. Pre-B lymphocytes can synthesize heavy chain in the absence of light chain, which then can allow the heavy ch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Complex
A protein complex or multiprotein complex is a group of two or more associated polypeptide chains. Protein complexes are distinct from multienzyme complexes, in which multiple catalytic domains are found in a single polypeptide chain. Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions. These complexes are a cornerstone of many (if not most) biological processes. The cell is seen to be composed of modular supramolecular complexes, each of which performs an independent, discrete biological function. Through proximity, the speed and selectivity of binding interactions between enzymatic complex and substrates can be vastly improved, leading to higher cellular efficiency. Many of the techniques used to enter cells and isolate proteins are inherently disruptive to such large complexes, complicating the task of determining the components of a complex. Examples of protein complexes include the p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Function
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell (biology)
The cell is the basic structural and functional unit of life forms. Every cell consists of a cytoplasm enclosed within a membrane, and contains many biomolecules such as proteins, DNA and RNA, as well as many small molecules of nutrients and metabolites.Cell Movements and the Shaping of the Vertebrate Body in Chapter 21 of Molecular Biology of the Cell '' fourth edition, edited by Bruce Alberts (2002) published by Garland Science. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos. It is also common to describe small molecules such as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Granularity
Granularity (also called graininess), the condition of existing in granules or grains, refers to the extent to which a material or system is composed of distinguishable pieces. It can either refer to the extent to which a larger entity is subdivided, or the extent to which groups of smaller indistinguishable entities have joined together to become larger distinguishable entities. Precision and ambiguity Coarse-grained materials or systems have fewer, larger discrete components than fine-grained materials or systems. * A coarse-grained description of a system regards large subcomponents. * A fine-grained description regards smaller components of which the larger ones are composed. The concepts granularity, coarseness, and fineness are relative; and are used when comparing systems or descriptions of systems. An example of increasingly fine granularity: a list of nations in the United Nations, a list of all states/provinces in those nations, a list of all cities in those states, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electron Microscopy Data Bank
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. , the resource contained over 2,600 entries with a mean resolution of 15Å. Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface. Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB. EM Data Bank also provides the EMsearch search tool and data can also be queried at RCSB, EMB ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermal Fluctuations
In statistical mechanics, thermal fluctuations are random deviations of a system from its average state, that occur in a system at equilibrium.In statistical mechanics they are often simply referred to as fluctuations. All thermal fluctuations become larger and more frequent as the temperature increases, and likewise they decrease as temperature approaches absolute zero. Thermal fluctuations are a basic manifestation of the temperature of systems: A system at nonzero temperature does not stay in its equilibrium microscopic state, but instead randomly samples all possible states, with probabilities given by the Boltzmann distribution. Thermal fluctuations generally affect all the degrees of freedom of a system: There can be random vibrations (phonons), random rotations ( rotons), random electronic excitations, and so forth. Thermodynamic variables, such as pressure, temperature, or entropy, likewise undergo thermal fluctuations. For example, for a system that has an equilibriu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Elastic And Plastic Strain
In physics and materials science, plasticity, also known as plastic deformation, is the ability of a solid material to undergo permanent deformation, a non-reversible change of shape in response to applied forces. For example, a solid piece of metal being bent or pounded into a new shape displays plasticity as permanent changes occur within the material itself. In engineering, the transition from elastic behavior to plastic behavior is known as yielding. Plastic deformation is observed in most materials, particularly metals, soils, rocks, concrete, and foams. However, the physical mechanisms that cause plastic deformation can vary widely. At a crystalline scale, plasticity in metals is usually a consequence of dislocations. Such defects are relatively rare in most crystalline materials, but are numerous in some and part of their crystal structure; in such cases, plastic crystallinity can result. In brittle materials such as rock, concrete and bone, plasticity is caused pre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database Of Molecular Motions
The Database of Macromolecular Motions is a bioinformatics database and Software as a service, software-as-a-service tool that attempts to categorize macromolecular motions, sometimes also known as conformational change. It was originally developed by Mark Bender Gerstein, Mark B. Gerstein, Werner G. Krebs, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University. Discussion Since its introduction in the late 1990s, peer-reviewed papers on the database have received thousands of citations. The database has been mentioned in news articles in major scientific journals, book chapters, and elsewhere. Users can search the database for a particular motion by either protein name or Protein Data Bank ID number. Typically, however, users will enter the database via the Protein Data Bank, which often provides a hyperlink to the molmovdb entry for proteins found in both databases. The database includes a web-based tool (the Morph server) which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
