AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules. The method for the interaction map definition is described in the help page

Enter the PDB ID for the structure you want to analyze
(find it with )

(i.e. 1JTG)
or browse here a PDB-like file to upload

Optional parameters:
Enter distance to water
(default is 3.5A)
browse for a file listing the amino acids to be analyzed (no interface or cluster search will be made) input example
Check here to analyze Ala as main chain


D. Reichmann, M. Cohen, R. Abramovich, D. Lim, Dym O., N.C.J. Strynadka and G. Schreiber "Binding hot spots in the TEM1-BLIP interface in light of its modular architecture", J. Mol. Biol. 2007, 365(3):663-79, abstract.

For comments and questions email to Dana Reichmann

AquaProt by Asaf Carmi, Mati Cohen, Dana Reichmann, and Jaime Prilusky, 2007
Bioinformatics and Biological Computing
Weizmann Institute of Science