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Updated: Aug 15, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
Inferring protein domain interactions from databases of interacting proteins
Robert Riley1, Christopher Lee, Chiara Sabatti
1Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA. riley@mbi.ucla.edu
Domain Pair Exclusion Analysis (DPEA) infers protein domain interactions from protein interaction data. This method identified 3,005 high-confidence domain interactions, aiding future experimental discoveries.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Protein interactions are fundamental to cellular processes.
- Understanding domain interactions is key to deciphering protein function.
- Existing methods for inferring domain interactions have limitations.
Purpose of the Study:
- To introduce Domain Pair Exclusion Analysis (DPEA), a novel computational method.
- To infer high-confidence domain-domain interactions from large-scale protein interaction databases.
- To provide a tool for guiding experimental validation of novel domain interactions.
Main Methods:
- DPEA utilizes a log odds score (Eij) to quantify the confidence of domain interactions.
- Analyzed 177,233 potential domain interactions derived from 26,032 known protein interactions.
- Validated inferred interactions against known domain interactions in the Protein Data Bank.
Main Results:
- Successfully inferred 3,005 high-confidence domain-domain interactions.
- Demonstrated the method's ability to identify significant domain associations.
- The inferred interactions showed good agreement with experimentally validated data.
Conclusions:
- DPEA is an effective computational approach for predicting domain interactions.
- The method can uncover previously unrecognized domain interactions.
- DPEA serves as a valuable tool to prioritize experimental investigations in protein science.
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