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Due to increased activity in high-throughput structural genomics effortsaround the globe, there has been an accumulation of experimental protein 3Dstructures lacking functional annotation, thus creating a need forstructure-based protein function assignment methods. Computational predictionof ligand binding sites (LBS) is a well-established protein function assignmentmethod. Here we apply the specific LBS detection algorithm we recentlydescribed (Reyes, V.M. & Sheth, V.N., 2011; Reyes, V.M., 2015a) to some 801functionally unannotated experimental structures in the Protein Data Bank byscreening for the binding sites (BS) of 6 biologically important ligands: GTPin small Ras-type G-proteins, ATP in ser/thr protein kinases, sialic acid(SIA), retinoic acid (REA), and heme-bound and unbound (free) nitric oxide(hNO, fNO). Validation of the algorithm for the GTP- and ATP-binding sites hasbeen previously described in detail (ibid.); here, validation for the BSs ofthe 4 other ligands shows both good specificity and sensitivity. Of the 801structures screened, 8 tested positive for GTP binding, 61 for ATP binding, 35for SIA binding, 132 for REA binding, 33 for hNO binding, and 10 for fNObinding. Using the cutting plane and tangent sphere methods we describedpreviously, (Reyes, V.M., 2015b), we also determined the depth of burial of theLBSs detected above and compared the values with those from the respectivetraining structures, and the degree of similarity between the two values takenas a further validation of the predicted LBSs. Applying this criterion, we wereable to narrow down the predicted GTP-binding proteins to 2, the ATP-bindingproteins to 13, the SIA-binding proteins to 2, the REA-binding proteins to 14,the hNO-binding proteins to 4, and the fNO-binding proteins to 1. We believethis further criterion increases the confidence level of our LBS predictions.

Structure-Based Function Prediction of Functionally Unannotated  Structures in the PDB: Prediction of ATP, GTP, Sialic Acid, Retinoic Acid and  Heme-bound and -Unbound (Free) Nitric Oxide Protein Binding Sites