Accurate Protein–ATP Binding Site Prediction

ATPbind web-server

ATPbind is a meta-server approach to protein-ATP binding site prediction. Starting from given structure of query protein, ATPbind will identify the ATP-binding sites by using SVM to integrate the outputs of two template-based predictors, i.e., S-SITEatp (the extension of S-SITE) and TM-SITEatp (the extension of TM-SITE), and three discriminative sequence-driven features, i.e., position specific scoring matrix (PSSM), predicted secondary structure, and predicted solvent accessibility. Users are also allowed to input primary sequence, where I-TASSER will be used to generate 3D model first which are then fed into the ATPbind pipeline for protein-ATP binding site prediction. If the input is a sequence, we strongly suggest users to employ the I-TASSER server to model the 3D structure first, since the I-TASSER server used in ATPbind is not the newest one. After protein-ATP binding site prediction, the ATPbind server implements a new binding pocket clustering scheme, PocHunter (download PocHunter.pdf to see the details), to identify the pockets based on the predicted binding sites.