Maciej Dziubiński1, Paweł Daniluk2, Bogdan Lesyng2. 1. Department of Biophysics and CoE BioExploratorium, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland and. 2. 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.
Abstract
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: The ResiCon server is available at URL: http://dworkowa.imdik.pan.pl/EP/ResiCon. CONTACT: pawel@bioexploratorium.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: The ResiCon server is available at URL: http://dworkowa.imdik.pan.pl/EP/ResiCon. CONTACT: pawel@bioexploratorium.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.