An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures

A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is increasing rapidly. In addition, many of the structures deposited in an ensemble exhibit variation in only some regions of the structure, often with the majority of the structure remaining largely invariant across the family of structures. Therefore it is useful to determine the set of atoms whose positions are 'well defined' across an ensemble (also known as the 'core' atoms). We have developed a computer program, NMRCORE, which automatically defines (i) the core atoms, and (ii) the rigid body(ies), or domain(s), in which they occur. The program uses a sorted list of the variances in individual dihedral angles across the ensemble to define the core, followed by the automatic clustering of the variances in pairwise inter-atom distances across the ensemble to define the rigid body(ies) which comprise the core. The program is freely available via the World Wide Web (http://neon.chem.le.ac.uk/nmrcore/).