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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F20%3A00115070" target="_blank" >RIV/00216224:14330/20:00115070 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/protocol/10.1007%2F978-1-4939-9873-9_7" target="_blank" >https://link.springer.com/protocol/10.1007%2F978-1-4939-9873-9_7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-1-4939-9873-9_7" target="_blank" >10.1007/978-1-4939-9873-9_7</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

C - Kapitola v odborné knize

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/LQ1601" target="_blank" >LQ1601: CEITEC 2020</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2020

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název knihy nebo sborníku

Protein-Protein Interaction Networks

ISBN

9781493998722

Počet stran výsledku

14

Strana od-do

81-94

Počet stran knihy

291

Název nakladatele

Humana Press Inc

Místo vydání

New York, NY

Kód UT WoS kapitoly

000558678200008