The Database of Macromolecular Motions is a
bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
and
software-as-a-service
Software as a service (SaaS ) is a cloud computing service model where the provider offers use of application software to a client and manages all needed physical and software resources. SaaS is usually accessed via a web application. Unlike oth ...
tool that attempts to
categorize
macromolecular
A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physi ...
motions, sometimes also known as
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 othe ...
.
It was originally developed by
Mark B. Gerstein,
Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at
Yale University
Yale University is a Private university, private Ivy League research university in New Haven, Connecticut, United States. Founded in 1701, Yale is the List of Colonial Colleges, third-oldest institution of higher education in the United Stat ...
.
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
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
name or
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 a ...
ID number.
Typically, however, users will enter the database via 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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...
, 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 allows non-experts to animate and visualize certain types of protein
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 othe ...
through the generation of short movies. This system uses
molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scien ...
techniques to
interpolate
In the mathematical field of numerical analysis, interpolation is a type of estimation, a method of constructing (finding) new data points based on the range of a discrete set of known data points.
In engineering and science, one often has a ...
the structural changes between two different protein conformers and to generate a set of intermediate structures. A hyperlink pointing to the morph results is then emailed to the user.
The Morph Server was originally primarily a research tool rather than general molecular animation tool, and thus offered only limited user control over rendering, animation parameters, color, and point of view, and the original methods sometimes required a fair amount of CPU time to completion.
Since their initial introduction in 1996, the database and associated morph server have undergone development to try to address some of these shortcomings
as well as add new features, such as
Normal Mode
A normal mode of a dynamical system is a pattern of motion in which all parts of the system move sinusoidally with the same frequency and with a fixed phase relation. The free motion described by the normal modes takes place at fixed frequencies ...
Analysis. Other research grounds have subsequently developed alternative systems, such a
MovieMaker from the
University of Alberta
The University of Alberta (also known as U of A or UAlberta, ) is a public research university located in Edmonton, Alberta, Canada. It was founded in 1908 by Alexander Cameron Rutherford, the first premier of Alberta, and Henry Marshall Tory, t ...
.
[
]
Commercialization
Bioinformatics vendor DNASTAR has incorporated morphs from the database into its commercial Protean3D product.
See also
* Database of protein conformational diversity
Notes
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References
External links
The Database of Macromolecular Motions (molmovdb)MovieMaker from the University of Alberta
{{Webarchive, url=https://web.archive.org/web/20160124053957/http://wishart.biology.ualberta.ca/moviemaker/ , date=2016-01-24
Biological databases
Cloud applications
Biophysics
Protein classification