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1.  FINDSITE: a combined evolution/structure-based approach to protein function prediction 
Briefings in Bioinformatics  2009;10(4):378-391.
A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to protein function inference and ligand screening that can provide functional insights for a significant fraction of the ∼50% of ORFs of unassigned function in an average proteome. We then describe FINDSITE, a recently developed algorithm for ligand binding site prediction, ligand screening and molecular function prediction, which is based on binding site conservation across evolutionary distant proteins identified by threading. Importantly, FINDSITE gives comparable results when high-resolution experimental structures as well as predicted protein models are used.
doi:10.1093/bib/bbp017
PMCID: PMC2691936  PMID: 19324930
protein function prediction; ligand binding site prediction; virtual ligand screening; protein structure prediction; low-resolution protein structures

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