Abstract Summary: Proteins can adopt a variety of conformations. We present a simple server for scoring the agreement between 3D atomic structures and experimental envelopes obtained by atomic force microscopy. Three different structures of immunoglobulins (IgG) or blood coagulation factor V activated were tested and their agreement with several topographical surfaces was computed. This approach can be used to test structural variability within a family of proteins. Availability and implementation: DockAFM is available at http://biodev.cea.fr/dockafm. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.