DockAFM: benchmarking protein structures by docking under AFM topographs.
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.


METHODS
DockAFM is available at http://biodev.cea.fr/dockafm.
CEA, iBEB, Service de Biochimie et Toxicologie Nucléaire, F-30207 Bagnols sur Cèze, France.
Rui C
RC
Chaves
Jean-Luc
JL
Pellequer
D005165:Factor V / Q000737:chemistry*; D006801:Humans; D007074:Immunoglobulin G / Q000737:chemistry*; D018625:Microscopy, Atomic Force / Q000379:methods*; D011487:Protein Conformation; D012984:Software
D007074:Immunoglobulin G; D005165:Factor V