J 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.

Základní údaje

Originální název

COZOID: COntact ZOne IDentifier for visual analysis of protein-protein interactions

Autoři

FURMANOVÁ, Katarína (703 Slovensko, domácí), Jan BYŠKA (203 Česká republika), Eduard M. GRÖLLER (40 Rakousko), Ivan VIOLA (703 Slovensko), Jan PALEČEK (203 Česká republika, domácí) a Barbora KOZLÍKOVÁ (203 Česká republika, garant, domácí)

Vydání

BMC Bioinformatics, 2018, 1471-2105

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 2.511

Kód RIV

RIV/00216224:14330/18:00102549

Organizační jednotka

Fakulta informatiky

DOI

UT WoS

000429467300001

Klíčová slova anglicky

Contact zone;Protein-protein interaction;Visualization

Štítky

Příznaky

Mezinárodní význam, Recenzováno
Změněno: 27. 8. 2019 12:58, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

LQ1601, projekt VaV
Název: CEITEC 2020 (Akronym: CEITEC2020)
Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020
MUNI/M/0822/2015, interní kód MU
Název: Expressive Visualization of Protein Complexes
Investor: Masarykova univerzita, Expressive Visualization of Protein Complexes, INTERDISCIPLINARY - Mezioborové výzkumné projekty