ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins.
BACKGROUND
Structure of most proteins is flexible. Identification and analysis of intramolecular motions is a complex problem. Breaking a structure into relatively rigid parts, the so-called dynamic domains, may help comprehend the complexity of protein's mobility. We propose a new approach called ResiCon (Residue Contacts analysis), which performs this task by applying a data-mining analysis of an ensemble of protein configurations and recognizes dynamic domains, hinges and interfacial regions, by considering contacts between residues.


RESULTS
Dynamic domains found by ResiCon are more compact than those identified by two other popular methods: PiSQRD and GeoStaS. The current analysis was carried out using a known reference set of 30 NMR protein structures, as well as molecular dynamics simulation data of flap opening events in HIV-1 protease. The more detailed analysis of HIV-1 protease dataset shows that ResiCon identified dynamic domains involved in structural changes of functional importance.


METHODS
The ResiCon server is available at URL: http://dworkowa.imdik.pan.pl/EP/ResiCon.


BACKGROUND
pawel@bioexploratorium.pl


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and.
Maciej
M
Dziubiński
Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
Paweł
P
Daniluk
Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
Bogdan
B
Lesyng
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D016333:HIV Protease / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D017434:Protein Structure, Tertiary; D012984:Software; D013269:Stochastic Processes
D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1