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Similar neural network models based on single sequence and evolutionary profiles of residues have been successfully used in the past for predicting secondary structure, solvent accessibility, protein-, DNA- and carbohydrate- binding sites. ATP is a ubiquitous ligand in all living-systems, involved in most biological functions requiring energy and charge transfer. Prediction of ATP-binding site from single sequences and their evolutionary profiles at a high throughput rate can be used at genomic level as well as quick clues for site-directed mutagenesis experiments. We have developed a method for such predictions to demonstrate yet another application of sequence-base prediction algorithms using neural networks. This method can achieve 81% sensitivity and 69% specificity which are mutually adjustable in a wide range on a three-fold cross-validation data set.