Prediction of binding sites of the Hsp70 chaperone DnaK

HSP70 chaperones assist protein folding by ATP-dependent association with linear peptide segments of folding intermediates. The paradigm for the molecular mechanism is the E. coli homologue DnaK. The principles for substrate selection are similar for most Hsp70s due to conservation of the substrate binding cavity. DnaK recognises short segments of up to 4-5 hydrophobic amino acids, in particular Leu. Flanking positively charged residues increase affinity. Based on a peptide binding study we developed an algorithm allowing prediction of DnaK binding sites with more than 80% accuracy.

Rüdiger S, Germeroth L, Schneider-Mergener J & Bukau B Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries. EMBO J. 1997; 16:1501-7. pdf

download the DnaK binding prediction algorithm (Note that the algorithm is designed for UNIX)
you can use the following example sequence
view instructions how to use the algorithm