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dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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new version for pdb2pdbqt #117

Closed zhangplpl closed 1 month ago

Hong-Rui commented 5 months ago

Supported new features:

  1. Unified protein residue topology templates for standard amino acids.
  2. Support 40 popular non-standard amino acid templates from Schrodinger's internal templates, including lots of C-ter and N-ters.
  3. Drop all MGLTools and openbabel dependencies in protein preprocessing parts.
  4. Support Receptor PDB standardizations prior to PDBQT format generation.
  5. Automatic AD4 map and autogrid4 runs in PDBQT generation process, with use of our own gpf and receptor clean algorithm, if ad4 options got specified.
  6. Support receptor preparation for covalent docking, and flex res.
  7. Support receptor preparation in case crystal water, cofactors are specified to be included.