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Updated: Apr 7, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
Published on: October 24, 2025
HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases
Albert Palleja1, Lars J Jensen2
1The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen N , Denmark ; The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen Ø , Denmark.
Abstract:
Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.
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