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. Author manuscript; available in PMC: 2016 Nov 1.
Published in final edited form as: Nat Protoc. 2016 Apr 14;11(5):905–919. doi: 10.1038/nprot.2016.051

Figure 2. Results of docking imatinib to its receptor in bound and apo conformations.

Figure 2

a. Redocking of flexible imatinib to rigid Abl (PDB entry 1iep) using AutoDock (purple) and AutoDock Vina (green). The X-ray crystallographic ligand position is in silver.

b. Cross docking of flexible imatinib to Abl (PDB entry 1fpu) with a single flexible residue side chain using AutoDock Vina (green). Note that Vina does not retain hydrogen atom positions during docking, so the threonine hydroxyl hydrogen is placed in a random position in the docked coordinate set.