Open AccessDynamite : a simple way to gain insight into protein motions
Author(s) -
Barrett C. Paul,
Hall Benjamin A.,
Noble Martin E. M.
Publication year - 2004
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444904019171
Subject(s) - pairwise comparison , principal component analysis , simple (philosophy) , computer science , component (thermodynamics) , covariance , motion (physics) , space (punctuation) , artificial intelligence , data mining , mathematics , physics , statistics , philosophy , epistemology , thermodynamics , operating system
A public web‐based facility to infer, analyse and graphically represent the likely modes of a protein motion, starting from a static structure, is presented. This facility is based on the use of CONCOORD to generate an ensemble of feasible protein structures that are subsequently analysed by principal component analysis to identify probable concerted motions. The user is returned the ensemble of feasible structures, together with associated analyses, including animations and graphical representations of both the principal component of the ensemble covariance and indicators of strongly correlated pairwise atomic motions. Whilst users are warned that completely reliable inferences about protein motion may be beyond even substantially more rigorous tools for exploring configurational space, it is hoped that the service will allow a much wider community to benefit from the insights that simple dynamic data may offer.