Molecular Movements Database
Help and Information Page

[ Morph Server FAQ | Morph Server description | Motion sets explained ]

The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits. The HingeMaster server predicts hinges in single protein structures using the FlexOracle, hNMb, TLSMD, StoneHinge, and other algorithms.

Copyright Statement

Unless otherwise notated, all pages in this database are copyright 1995-2003, Mark Gerstein, all rights reserved. In particular, please do not incorporate this database into other databases without prior permission of the author. Some of our algorithms, notably the HingeMaster and Conformation Explorer, have pending patents. Please use the citation below when refering to the database in print.

Citation Info:

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Open source and publicly available software used

This web server and many of the services it provides use Apache, Linux (SUSE), and mySQL. The HingeMaster and FlexOracle hinge predictors use TINKER, GROMACS, and FoldX, in addition to software mentioned elsewhere.


The NSF is acknowledged for support (award DBI-9723182).

Other documents about the database

Database formats

The database is now kept as a combination of XML files and MySQL tables, which allows maximum flexibility for programming and editing. Complete data sets are available on request from the authors.

New features in version 3.0

Hinge analysis and prediction
A variety of services have been added to identify hinge regions, either in single structures or morphs. A complete description of these is being prepared for publication.
Functional annotation
For structures where active site templates are available, these sites have been mapped onto the morph. We have also extended the searches to include homologous structures. GO (Gene Ontology) descriptions are now available for both motions and morphs.
Morphing with FRODA
FRODA is a new program from the Thorpe Lab (Arizona State) for generating physically plausible interpolations. It may be used instead of the traditional adiabatic mapping procedure from the morph submission page.
Improved multichain morphing
A new version of the Morph Server will handle multiple chains with non-identical sequences and large gaps. This allows interpolations to be obtained for structures that previously required significant manual alteration. Chain and residue numbering is preserved from the original PDB files, where possible.

Possible ways a motion can be classified

[D-s-2] Known Domain Motion, Shear Mechanism
[D-h-2] Known Domain Motion, Hinge Mechanism
[D-?-2] Known Domain Motion, Unclassifiable Mechanism
[D-n-2] Known Domain Motion, Neither Hinge nor Shear Mechanism
[D-f-2] Known Domain Motion, Partial Refolding of Structure
[D-s-1] Suspected Domain Motion, Shear Mechanism
[D-h-1] Suspected Domain Motion, Hinge Mechanism
[D-?-1] Suspected Domain Motion, Unclassifiable Mechanism
[D-n-1] Suspected Domain Motion, Neither Hinge nor Shear Mechanism
[F-s-2] Known Fragment Motion, Shear Mechanism
[F-h-2] Known Fragment Motion, Hinge Mechanism
[F-?-2] Known Fragment Motion, Unclassifiable
[F-n-2] Known Fragment Motion, Neither Hinge nor Shear Mechanism
[F-s-1] Suspected Fragment Motion, Shear Mechanism
[F-h-1] Suspected Fragment Motion, Hinge Mechanism
[F-?-1] Suspected Fragment Motion, Unclassifiable
[F-n-1] Suspected Fragment Motion, Neither Hinge nor Shear Mechanism
[S-a-2] Known Subunit Motion, Involving Allostery
[S-n-2] Known Subunit Motion, Not Involving Allostery
[S-a-1] Suspected Subunit Motion, Involving Allostery
[S-n-1] Suspected Subunit Motion, Not Involving Allostery
[F----] Known, Notably Motionless Proteins (fragment)
[D----] Known, Notably Motionless Proteins (domain)
[S----] Known, Notably Motionless Proteins (subunit)
[C----] Complex Motion
[N-R-1] Suspected RNA Motion
[N-R-2] Known RNA Motion
[N-D-1] Suspected DNA Motion
[N-D-2] Known DNA Motion


The original database was created by
Mark Gerstein and Werner Krebs. The original Morph Server was written by Werner Krebs. The server was extended to handle multiple chains by Flores, Echols, Hespenheide, Wells, Thorpe, and Gerstein. The current version is maintained by Sam Flores, with assistance from Nat Echols. The HingeMaster server was written by Samuel Flores and Mark Gerstein, with help and certain pieces of code from Kevin Keating, Jay Painter, Ethan Merritt, and Leslie Kuhn. Past contributors include Vadim Alexandrov,Yu (Brandon) Xia, Ursula Lehnert, Neil Voss, Julian Graham, Michael Barnett, Haiyuan Yu, Mickey Kataria, and Britt Park and Duncan Milburn.
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Copyright 1995-2001 M. Gerstein, W. G. Krebs
Last modified 8-24-01