ADapt is not released yet. These pages describe a test version.
ADapt works in a web browser. It takes a PDB entry to receptor and ligand files ready for docking with AutoDock4, AutoDock Vina, AutoDockFR and AutoDock CrankPep.
A PDB file records a crystallographic experiment, not a molecule ready for docking. Preparing a receptor from it means making a series of choices: the asymmetric unit or a biological assembly, what to do with missing atoms and residues, which alternate location to keep, which cofactors, ligands, metals and waters to keep or remove. Most of these choices depend on where a fragment sits relative to the pocket you plan to dock into, so they are best made while looking at the structure.
ADapt reads a PDB file, or fetches it from the RCSB, and analyses it with ADFR’s own code, the same code as the PDB analyzer of AGFRgui. It builds every biological assembly the file defines, classifies every residue by what it is and what it needs, proposes the usual choices as defaults, and shows each chain as a tree linked to a 3D view.
License
ADapt is distributed under the Sannerlab MIT-like Source-Available License.