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Updated: Aug 24, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein ranking: from local to global structure in the protein similarity network
Jason Weston1, Andre Elisseeff, Dengyong Zhou
1NEC Laboratories America, 4 Independence Way, Princeton, NJ 08540, USA.
Abstract:
Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a precomputed, weighted network. The resulting ranking algorithm, evaluated by using a human-curated database of protein structures, is efficient and provides significantly better rankings than a local network search algorithm such as psi-blast.
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