Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool
The result's identifiers
Result code in 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>
Result on the web
<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>
Alternative languages
Result language
angličtina
Original language name
Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool
Original language description
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.
Czech name
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Czech description
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Classification
Type
C - Chapter in a specialist book
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/LQ1601" target="_blank" >LQ1601: CEITEC 2020</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Book/collection name
Protein-Protein Interaction Networks
ISBN
9781493998722
Number of pages of the result
14
Pages from-to
81-94
Number of pages of the book
291
Publisher name
Humana Press Inc
Place of publication
New York, NY
UT code for WoS chapter
000558678200008