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.

Základní údaje

Originální název

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

Autoři

BYŠKA, Jan (203 Česká republika, domácí), Adam JURČÍK (203 Česká republika, domácí), Katarína FURMANOVÁ (703 Slovensko, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Jan PALEČEK (203 Česká republika, garant, domácí)

Vydání

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

Nakladatel

Humana Press Inc

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Kód RIV

RIV/00216224:14330/20:00115070

Organizační jednotka

Fakulta informatiky

ISBN

978-1-4939-9872-2

DOI

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

UT WoS

000558678200008

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 12. 2020 08:44, Mgr. Marie Šípková, DiS.

Anotace

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.

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

Citovat

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

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