Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Pruning PPIs with domain-domain interactions

SG Shishir K. Gupta
MS Mugdha Srivastava
ÖO Özge Osmanoglu
TD Thomas Dandekar
request Request a Protocol
ask Ask a question
Favorite

The amino acid sequences of non-redundant preliminary PPIs were extracted and domains were assigned to them using Pfam version 27.062. The list of non-redundant domain-domain interactions was prepared from the meta-databases Domine63, DIMA 3.064 and IDDI database65. These use complexes available in the Protein Data Bank (PDB)66 to identify by interacting domains the Pfam families containing these domains. These Pfam families are then predicted to be interacting. This list was used to parse the template PPIs. All interactions were categorized whether they are supported (good interactions, used for further filtering steps) or not by domain-domain interactions (DDIs).

Copyright and License information: The Author(s) ©2020
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A