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Updated: Jun 3, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD)
Michael S Livstone1, Rose Oughtred, Sven Heinicke
1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
Abstract:
Inferring a protein's function by homology is a powerful tool for biologists. The Princeton Protein Orthology Database (P-POD) offers a simple way to visualize and analyze the relationships between homologous proteins in order to infer function. P-POD contains computationally generated analysis distinguishing orthologs from paralogs combined with curated published information on functional complementation and on human diseases. P-POD also features an applet, Notung, for users to explore and modify phylogenetic trees and generate their own ortholog/paralogs calls. This unit describes how to search P-POD for precomputed data, how to find and use the associated curated information from the literature, and how to use Notung to analyze and refine the results.
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