MolMovDB: analysis and visualization of conformational change and structural flexibility

Abstract

The Database of Macromolecular Movements (http://MolMovDB.org) is a collection of data and software pertaining to flexibility in protein and RNA structures. The database is organized into two parts. Firstly, a collection of 'morphs' of solved structures representing different states of a molecule provides quantitative data for flexibility and a number of graphical representations. Secondly, a classification of known motions according to type of conformational change (e.g. 'hinged domain' or 'allosteric') incorporates textual annotation and information from the literature relating to the motion, linking together many of the morphs. A variety of subsets of the morphs are being developed for use in statistical analyses. In particular, for each subset it is possible to derive distributions of various motional quantities (e.g. maximum rotation) that can be used to place a specific motion in context as being typical or atypical for a given population. Over the past year, the database has been greatly expanded and enhanced to incorporate new structures and to improve the quality of data. The 'morph server', which enables users of the database to add new morphs either from their own research or the PDB, has also been enhanced to handle nucleic acid structures and multi-chain complexes.

Figure 1

(A) Schema of the database, showing flow of information and relationship between motions and morphs. The ideal morph for each motion, where available, is shown with bold highlighting. (B) Page describing an individual morph. At the top is a listing of movies and images associated with the morph, followed by more elaborate representations. Complete trajectories are available for download either as a collection of files or as a single PDB file with multiple MODEL records. A comprehensive listing of statistics generated by the server appears below, along with the sequence alignment used as reference when generating the morph (not shown).

Figure 1

(A) Schema of the database, showing flow of information and relationship between motions and morphs. The ideal morph for each motion, where available, is shown with bold highlighting. (B) Page describing an individual morph. At the top is a listing of movies and images associated with the morph, followed by more elaborate representations. Complete trajectories are available for download either as a collection of files or as a single PDB file with multiple MODEL records. A comprehensive listing of statistics generated by the server appears below, along with the sequence alignment used as reference when generating the morph (not shown).

Figure 2

A representative distribution of a statistic from one subset of the database. The subset encompasses all user-submitted morphs. The statistic used is the RMS deviation (in Angstroms) between start and end frames of the ‘2nd core’, the moving part of the protein, as calculated by our sieve-fitting procedure. The positions of several well-studied motions in this distribution are highlighted and labeled with their respective RMSD and percentile values.