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COZOID: contact zone identifier for visual analysis of protein-protein interactions

Katarína Furmanová, Jan Byška, Eduard M. Gröller, Ivan Viola, Jan J. Paleček, Barbora Kozlíková
2018 BMC Bioinformatics  
Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes.  ...  The exploration of the vast space of possible mutual configurations of interacting proteins and their contact zones is very time consuming and requires the proteomic expert knowledge.  ...  Acknowledgements We acknowledge the members of Palecek lab for their participation in the COZOID testing.  ... 
doi:10.1186/s12859-018-2113-6 pmid:29625561 pmcid:PMC5889581 fatcat:5gqfknjofbbkxibz3qarshydky

Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein Complexes

Katarina Furmanova, Adam Jurcik, Barbora Kozlikova, Helwig Hauser, Jan Byska
2019 IEEE Transactions on Visualization and Computer Graphics  
Our approach takes advantage of the hierarchical structure of the data - from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting  ...  Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels.  ...  Parts of this work were done in the context of the VIDI project, which is supported by Bergens Forskningsstiftelse, the Mohn Medical Imaging and Visualization Center (MMIV), and the University of Bergen  ... 
doi:10.1109/tvcg.2019.2934333 pmid:31425101 fatcat:v67mqmdoqzenvfwhnehrttz6cm

A Single Conserved Amino Acid Residue as a Critical Context-Specific Determinant of the Differential Ability of Mdm2 and MdmX RING Domains to Dimerize

Pavlína Kosztyu, Iva Slaninová, Barbora Valčíková, Amandine Verlande, Petr Müller, Jan J. Paleček, Stjepan Uldrijan
2019 Frontiers in Physiology  
We performed a systematic mutational analysis of human Mdm2, exchanging parts of the RING with the corresponding MdmX sequence, to identify the molecular determinants of this difference.  ...  Mdm2 and MdmX are related proteins serving in the form of the Mdm2 homodimer or Mdm2/MdmX heterodimer as an E3 ubiquitin ligase for the tumor suppressor p53.  ...  ACKNOWLEDGMENTS We thank Karen Vousden, Robert Ludwig, Donna George, Arnie Levine, Ted Dawson, and Zhi-Min Yuan for the expression plasmids and Borivoj Vojtesek for the anti-p53 antibody.  ... 
doi:10.3389/fphys.2019.00390 pmid:31024344 pmcid:PMC6465955 fatcat:33ljrzq4ybbf3o4uo4vuxe66i4