The Database of Macromolecular Motions is a

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

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 sp ...

and

software-as-a-service Software as a service (SaaS ) is a software licensing and delivery model in which software is licensed on a subscription basis and is centrally hosted. SaaS is also known as "on-demand software" and Web-based/Web-hosted software. SaaS is cons ...

tool that attempts to categorize

macromolecular A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The ...

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 oth ...

. 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 research university in New Haven, Connecticut. Established in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and among the most prestigious in the wo ...

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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

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. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

ID number. Typically, however, users will enter the database via the

, 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

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 sci ...

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 n ...

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,"A Gentleman of Strathcona – Alexander Cameron Rutherfor ...

Commercialization

Bioinformatics vendor

DNASTAR DNASTAR is a global bioinformatics software company incorporated in 1984 that is headquartered in Madison, Wisconsin. DNASTAR develops and sells software for sequence analysis in the fields of genomics, molecular biology, and structural biology. ...

has incorporated morphs from the database into its commercial Protean3D product. The connection between DNASTAR and the authors of the database, if any, is not immediately clear.

Notes

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References

{{reflist

External links

The Database of Macromolecular Motions (molmovdb)MovieMaker from the University of Alberta
Biological databases Cloud applications Biophysics Protein classification

Discussion

Commercialization

See also

Notes

References

External links