Database of Molecular Motions
Encyclopedia
The Database of Macromolecular Motions (molmovdb) is a bioinformatics
database
that attempts to
categorize macromolecular motions, sometimes also known as conformational change
.
It was original developed by Mark B. Gerstein
, Samuel Flores, Werner Krebs, and Nat Echols in
the Molecular Biophysics & Biochemistry Department at Yale University
.
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 allows
non-experts to
animate and visualize certain types of protein conformational change
through the generation of short movies (8).
This system uses molecular modelling
techniques to interpolate the structural changes
between two different protein conformers and to generate a set of plausible 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
Analysis.
Other research grounds have subsequently developed alternative systems, such as MovieMaker from the University of Alberta
.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
database
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
that attempts to
categorize macromolecular motions, sometimes also known as conformational change
Conformational change
A macromolecule is usually flexible and dynamic. It can change its shape 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...
.
It was original developed by Mark B. Gerstein
Mark Bender Gerstein
Professor Mark B. Gerstein is an American scientist working in bioinformatics. , he is co-director of the Yale Computational Biology and Bioinformatics program, andAlbert L...
, Samuel Flores, Werner Krebs, and Nat Echols in
the Molecular Biophysics & Biochemistry Department at Yale University
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
.
Users can search the database for a particular motion by either protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
name or Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
ID number. Typically,
however, users will enter the database via the Protein Data Bank
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, 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
Conformational change
A macromolecule is usually flexible and dynamic. It can change its shape 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...
through the generation of short movies (8).
This system uses molecular modelling
Molecular modelling
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
techniques to interpolate the structural changes
between two different protein conformers and to generate a set of plausible 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
Normal mode
A normal mode of an oscillating 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 frequencies of the normal modes of a system are known as its natural frequencies or resonant frequencies...
Analysis.
Other research grounds have subsequently developed alternative systems, such as MovieMaker from the University of Alberta
University of Alberta
The University of Alberta is a public research university located in Edmonton, Alberta, Canada. Founded in 1908 by Alexander Cameron Rutherford, the first premier of Alberta and Henry Marshall Tory, its first president, it is widely recognized as one of the best universities in Canada...
.
External links
- The Database of Macromolecular Motions (molmovdb)
- Book Chapter on Protein Motions from website of RH Austin at Princeton UniversityPrinceton UniversityPrinceton University is a private research university located in Princeton, New Jersey, United States. The school is one of the eight universities of the Ivy League, and is one of the nine Colonial Colleges founded before the American Revolution....