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

Katarína Furmanová, Jan Byska, Meister Eduard Gröller, Ivan Viola, Jan J. Paleček, Barbora Kozlikova
COZOID: contact zone identifier for visual analysis of protein-protein interactions
BMC Bioinformatics, (19:125 ):1-25, April 2018. [image] [Paper]

Information

Abstract

Background: Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding thestructure and function of protein complexes. The exploration of the vast space of possible mutual configurations ofinteracting 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 guidedexploration of PPI configuration space. It helps proteomic experts to select the most relevant configurations andexplore their contact zones at different levels of detail. The system integrates a set of methods that follow and supportthe workflow of proteomics experts. The first visual abstraction method, the Matrix view, is based on customizedinteractive heat maps and provides the users with an overview of all possible residue-residue contacts in all PPIconfigurations and their interactive filtering. In this step, the user can traverse all input PPI configurations and obtain anoverview of their interacting amino acids. Then, the models containing a particular pair of interacting amino acids canbe selectively picked and traversed. Detailed information on the individual amino acids in the contact zones and theirproperties is presented in the Contact-Zone list-view. The list-view provides a comparative tool to rank the best modelsbased on the similarity of their contacts to the template-structure contacts. All these techniques are interactivelylinked with other proposed methods, the Exploded view and the Open-Book view, which represent individualconfigurations in three-dimensional space. These representations solve the high overlap problem associated withmany configurations. Using these views, the structural alignment of the best models can also be visually confirmed.

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BibTeX

@article{Furmanova_2018,
  title =      "COZOID: contact zone identifier for visual analysis of
               protein-protein interactions",
  author =     "Katar\'{i}na  Furmanov\'{a} and Jan Byska and Meister Eduard
               Gr\"{o}ller and Ivan Viola and Jan J.  Pale\v{c}ek and
               Barbora Kozlikova",
  year =       "2018",
  abstract =   "Background: Studying the patterns of protein-protein
               interactions (PPIs) is fundamental for understanding
               thestructure and function of protein complexes. The
               exploration of the vast space of possible mutual
               configurations ofinteracting 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 guidedexploration of PPI configuration space. It helps
               proteomic experts to select the most relevant configurations
               andexplore their contact zones at different levels of
               detail. The system integrates a set of methods that follow
               and supportthe workflow of proteomics experts. The first
               visual abstraction method, the Matrix view, is based on
               customizedinteractive heat maps and provides the users with
               an overview of all possible residue-residue contacts in all
               PPIconfigurations and their interactive filtering. In this
               step, the user can traverse all input PPI configurations and
               obtain anoverview of their interacting amino acids. Then,
               the models containing a particular pair of interacting amino
               acids canbe selectively picked and traversed. Detailed
               information on the individual amino acids in the contact
               zones and theirproperties is presented in the Contact-Zone
               list-view. The list-view provides a comparative tool to rank
               the best modelsbased on the similarity of their contacts to
               the template-structure contacts. All these techniques are
               interactivelylinked with other proposed methods, the
               Exploded view and the Open-Book view, which represent
               individualconfigurations in three-dimensional space. These
               representations solve the high overlap problem associated
               withmany configurations. Using these views, the structural
               alignment of the best models can also be visually confirmed.",
  month =      apr,
  doi =        " 10.1186/s12859-018-2113-6",
  journal =    "BMC Bioinformatics",
  number =     "19:125 ",
  pages =      "1--25",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2018/Furmanova_2018/",
}