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We report a template-based method, LT-scanner, which scans the human proteome using protein structural alignment to identify proteins that are likely to bind ligands that are present in experimentally determined complexes. A scoring function that rapidly accounts for binding site similarities between the template and the proteins being scanned is a crucial feature of the method. The overall approach is first tested based on its ability to predict the residues on the surface of a protein that are likely to bind small-molecule ligands. The algorithm that we present, LBias, is shown to compare very favorably to existing algorithms for binding site residue prediction. LT-scanner's performance is evaluated based on its ability to identify known targets of Food and Drug Administration (FDA)- approved drugs and it too proves to be highly effective. The specificity of the scoring function that we use is demonstrated by the ability of LT-scanner to identify the known targets of FDA-approved kinase inhibitors based on templates involving other kinases. Combining sequence with structural information further improves LTscanner performance. The approach we describe is extendable to the more general problem of identifying binding partners of known ligands even if they do not appear in a structurally determined complex, although this will require the integration of methods that combine protein structure and chemical compound databases. [ABSTRACT FROM AUTHOR]