Visual Analysis of Protein–Protein Interaction Docking Models
Using COZOID Tool

C 2020

Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool

BYŠKA, Jan; Adam JURČÍK; Katarína FURMANOVÁ; Barbora KOZLÍKOVÁ; Jan PALEČEK et. al.

Basic information

Original name

Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool

Authors

BYŠKA, Jan (203 Czech Republic, belonging to the institution); Adam JURČÍK (203 Czech Republic, belonging to the institution); Katarína FURMANOVÁ (703 Slovakia, belonging to the institution); Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Jan PALEČEK (203 Czech Republic, guarantor, belonging to the institution)

Edition

1. vyd. New York, NY, Protein-Protein Interaction Networks, p. 81-94, 14 pp. Methods in Molecular Biology, vol. 2074, 2020

Publisher

Humana Press Inc

Other information

Language

English

Type of outcome

Chapter(s) of a specialized book

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14330/20:00115070

Organization unit

Faculty of Informatics

ISBN

978-1-4939-9872-2

DOI

http://dx.doi.org/10.1007/978-1-4939-9873-9_7

UT WoS

000558678200008

EID Scopus

2-s2.0-85072917694

Keywords in English

Protein–protein interactions;Contact zone;Contact residue;Multiple sequence alignment;Conservation rate;Protein docking;COZOID tool;Visual selection

Abstract

V originále

Networks of protein–protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conservation information is utilized in template-based approaches, like protein structure modeling or docking. Here we use the combination of the template-free docking method with conservation-based selection of the best docking model using our newly developed COZOID tool. We describe a step-by-step protocol for visual selection of docking models, based on their similarity to the original protein complex structure. Using the COZOID tool, we first analyze contact zones of the original complex structure and select contact amino acids for docking restraints. Then we model and dock the homologous proteins. Finally, we utilize different analytical modes of our COZOID tool to select the docking models most similar to the original complex structure.

Links

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

MUNI/M/0822/2015, interní kód MU

Name: Expressive Visualization of Protein Complexes

Investor: Masaryk University, INTERDISCIPLINARY - Interdisciplinary research projects

Cite

BYŠKA, Jan; Adam JURČÍK; Katarína FURMANOVÁ; Barbora KOZLÍKOVÁ and Jan PALEČEK. Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool. In Stefan Canzar, Francisca Rojas Ringeling. Protein-Protein Interaction Networks. 1st ed. New York, NY: Humana Press Inc, 2020, p. 81-94. Methods in Molecular Biology, vol. 2074. ISBN 978-1-4939-9872-2. Available from: https://dx.doi.org/10.1007/978-1-4939-9873-9_7.

@inbook{1550016,
   author = {Byška, Jan and Jurčík, Adam and Furmanová, Katarína and Kozlíková, Barbora and Paleček, Jan},
   address = {New York, NY},
   booktitle = {Protein-Protein Interaction Networks},
   doi = {http://dx.doi.org/10.1007/978-1-4939-9873-9_7},
   edition = {1},
   editor = {Stefan Canzar, Francisca Rojas Ringeling},
   keywords = {Protein–protein interactions;Contact zone;Contact residue;Multiple sequence alignment;Conservation rate;Protein docking;COZOID tool;Visual selection},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York, NY},
   isbn = {978-1-4939-9872-2},
   pages = {81-94},
   publisher = {Humana Press Inc},
   title = {Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool},
   url = {https://link.springer.com/protocol/10.1007%2F978-1-4939-9873-9_7},
   year = {2020}
}

TY  - CHAP
ID  - 1550016
AU  - Byška, Jan - Jurčík, Adam - Furmanová, Katarína - Kozlíková, Barbora - Paleček, Jan
PY  - 2020
TI  - Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool
VL  - Methods in Molecular Biology, vol. 2074
PB  - Humana Press Inc
CY  - New York, NY
SN  - 9781493998722
KW  - Protein–protein interactions;Contact zone;Contact residue;Multiple sequence alignment;Conservation rate;Protein docking;COZOID tool;Visual selection
UR  - https://link.springer.com/protocol/10.1007%2F978-1-4939-9873-9_7
L2  - https://link.springer.com/protocol/10.1007%2F978-1-4939-9873-9_7
N2  - Networks of protein–protein interactions (PPI) constitute either stable or transient complexes in every cell. Most of the cellular complexes keep their function, and therefore stay similar, during evolution. The evolutionary constraints preserve most cellular functions via preservation of protein structures and interactions. The evolutionary conservation information is utilized in template-based approaches, like protein structure modeling or docking. Here we use the combination of the template-free docking method with conservation-based selection of the best docking model using our newly developed COZOID tool. We describe a step-by-step protocol for visual selection of docking models, based on their similarity to the original protein complex structure. Using the COZOID tool, we first analyze contact zones of the original complex structure and select contact amino acids for docking restraints. Then we model and dock the homologous proteins. Finally, we utilize different analytical modes of our COZOID tool to select the docking models most similar to the original complex structure.
ER  -

BYŠKA, Jan; Adam JURČÍK; Katarína FURMANOVÁ; Barbora KOZLÍKOVÁ and Jan PALEČEK. Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool. In Stefan Canzar, Francisca Rojas Ringeling. \textit{Protein-Protein Interaction Networks}. 1st ed. New York, NY: Humana Press Inc, 2020, p.~81-94. Methods in Molecular Biology, vol. 2074. ISBN~978-1-4939-9872-2. Available from: https://dx.doi.org/10.1007/978-1-4939-9873-9\_{}7.

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