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.
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.
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View an example of output]
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List the benchmark dataset]
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Download the benchmark dataset]
References:
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Jun Hu, Yang Li, Yang Zhang, Dongjun Yu.
ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons.
Journal of Chemical Information and Modeling, 58(2): 501-510 (2018).
(Download PDF and
Support Information).
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