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Molecular Movements Database Help and Information Page

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.

Contents

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

  • The citation for the FlexOracle hinge predictor is SC Flores, MB Gerstein (2007). BMC Bioinformatics 8: 215.
  • The current citation for the morph server (which explains the CNS and FRODA multi-chain morph engines and other new features) is Flores, Echols, Milburn, Hespenheide, Keating, Lu, Wells, Yu, Thorpe, Gerstein (2006). Nucleic Acids Res. 34:D296-301.
  • The citation for the single-chain Morph Server is Krebs and Gerstein (2000). Nucleic Acids Res. 28:1665-75. If you reproduce movies from our site, please cite both of the above articles.
  • The original publication of the database was Gerstein and Krebs (1998). Nucleic Acids Res. 26:4280-90.
  • If you use our movies in PowerPoint, etc., please cite us as "The Yale Morph Server (http://molmovdb.org)". For any of the newer color movies, you should also cite the [ http://pymol.sourceforge.net/ PYMOL] molecular graphics system.
  • If you use the FRODA-LITE option on our morph server, please cite Wells S., Menor S., Hespenheide B.M and Thorpe M.F. (2005) Constrained Geometric Simulation of Diffusive Motion in Proteins. Physical Biology 2, S127-S136. More information and services related to FIRST/FRODA are available at Flexweb.
  • If your work makes use of the Catalytic Site Atlas gallery on our movie.cgi page, or the 'Highlight active sites' button on our morph.cgi page, please cite Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton (2004) Nucleic Acids Res. 32(Database Issue):D129-133.

Related papers

  • SC Flores, LJ Lu, J Yang, N Carriero, MB Gerstein (2007). "Hinge Atlas: relating protein sequence to sites of structural flexibility." BMC Bioinformatics 8: 167. full text
  • Echols, Milburn, and Gerstein (2003). Nucleic Acids Res. 31:478-82.
  • M Gerstein, A Lesk, C Chothia (1994). "Structural Mechanisms for Domain Movements in Proteins," Biochemistry 33: 6739-6749. (the basis for the original database)
  • M Gerstein, R Jansen, T Johnson, J Tsai & W Krebs (1999). "Studying Macromolecular Motions in a Database Framework: from Structure to Sequence," Rigidity theory and applications (ed. M F Thorpe & P M Duxbury, Kluwer Academic/Plenum Publishers), pp. 401-442. full text (a review article describing protein motions)
  • WG Krebs, J Tsai, V Alexandrov, N Echols, J Junker, R Jansen and M Gerstein (2001), "Studying Protein Flexibility in a Statistical Framework: Tools and Databases for Analyzing Structures and Approaches for Mapping this onto Sequences," Methods in Enzymology (in press). full text (practical discussion of computational analysis of protein motions)
  • WG Krebs, V Alexandrov, CA Wilson, N Echols, H Yu, M Gerstein (2002). Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48: 682-95. full text (in-depth analysis of large set of morphs)

Open source and publicly available software used

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

Support

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. Some sets of motion pairs are available for batch download at list.txt.gz

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

Authors

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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