Abstract Motivation: The use of allosteric modulators as preferred therapeutic agents against classic orthosteric ligands has colossal advantages, including higher specificity, fewer side effects and lower toxicity. Therefore, the computational prediction of allosteric sites in proteins is receiving increased attention in the field of drug discovery. Allosite is a newly developed automatic tool for the prediction of allosteric sites in proteins of interest and is now available through a web server. Availability: The Allosite server and tutorials are freely available at http://mdl.shsmu.edu.cn/AST Contact: jian.zhang@sjtu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.