Abstract: The present invention features methods and compositions for production of persistent acyl phosphate analogues (e.g., aspartyl phosphate analogues) using beryllofluoride (BeFx), as well as polypeptides comprising such an acyl phosphate analogue and antibodies that specifically bind to these polypeptides. The invention further features methods of using BeFx analogues in screening assays to identify candidate agent compounds that modulate activity of polypeptides that normally exhibit activity due to the presence of an acyl phosphate linkage (e.g., a phosphorylated aspartate residue as in, e.g., polypeptides involved in signal transduction, polypeptides involved in ion transport across biological membranes, phosphotransferases, etc.). The BeFx polypeptide analogues can also be used to facilitate determination of the structure of the corresponding phosphorylated polypeptide and in rationale drug design.