Detailed Information on Publication Record
2018
COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions
FURMANOVÁ, Katarína, Jan BYŠKA, Eduard M. GRÖLLER, Ivan VIOLA, Jan PALEČEK et. al.Basic information
Original name
COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions
Authors
FURMANOVÁ, Katarína (703 Slovakia, belonging to the institution), Jan BYŠKA (203 Czech Republic), Eduard M. GRÖLLER (40 Austria), Ivan VIOLA (703 Slovakia), Jan PALEČEK (203 Czech Republic, belonging to the institution) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution)
Edition
BMC Bioinformatics, 2018, 1471-2105
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 2.511
RIV identification code
RIV/00216224:14330/18:00102549
Organization unit
Faculty of Informatics
UT WoS
000429467300001
Keywords in English
Contact zone;Protein-protein interaction;Visualization
Tags
International impact, Reviewed
Změněno: 27/8/2019 12:58, RNDr. Pavel Šmerk, Ph.D.
Abstract
V originále
BACKGROUND: 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. RESULTS: In this paper, we propose a novel tool containing a set of visual abstraction techniques for the guided exploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations and explore their contact zones at different levels of detail. The system integrates a set of methods that follow and support the workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customized interactive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPI configurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain an overview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids can be selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and their properties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best models based on the similarity of their contacts to the template-structure contacts. All these techniques are interactively linked with other proposed methods, the Exploded view and the Open-Book view, which represent individual configurations in three-dimensional space. These representations solve the high overlap problem associated with many configurations. Using these views, the structural alignment of the best models can also be visually confirmed. CONCLUSIONS: We developed a system for the exploration of large sets of protein-protein complexes in a fast and intuitive way. The usefulness of our system has been tested and verified on several docking structures covering the three major types of PPIs, including coiled-coil, pocket-string, and surface-surface interactions. Our case studies prove that our tool helps to analyse and filter protein-protein complexes in a fraction of the time compared to using previously available techniques.
Links
| LQ1601, research and development project |
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| MUNI/M/0822/2015, interní kód MU |
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