AutoDock CrankPep (ADCP) is a specialized docking engine for peptides that uses a protein folding technique along with AutoDock’s efficient rigid receptor representation. It utilizes a Monte-Carlo search to fold the peptide while optimizing its interaction with the receptor, resulting in docked peptides. ADCP can handle peptides provided as a sequence string and has shown success with peptides of up to 20 amino acids.

In version 1.1, several improvements have been made, including support for non-standard amino acids and the ability to minimize docked poses using OpenMM. The changes include:

1. Streamlined output: Docked poses are now saved in a single multi-model PDB file named “xxx_out.pdb,” where “xxx” is the docking job name (or a default name) and a summary file named “xxx_summary.dlg” is generated.
2. Improved representation: Docked poses now include all-atom side chain representations, rather than a rotamer index.
3. User-defined number of docked poses: Users can set the number of docked poses using the “-m” or “–nmodes” command line option.
4. Command line changes: The target file specification has changed to “-T,” and it can accept a .trg file or a folder containing a .trg file. A new option, “-k,” allows users to keep calculation details.
5. Rotamer libraries: Rotamers for amino acid sidechains are loaded from text files with .lib extension, and system rotamer libraries can be specified using the “-L” option.
6. Support for non-standard amino acids: Version 1.1 has been modified to facilitate adding support for non-standard amino acids, allowing for the addition of rotamers for modified sidechains without recompiling the code. The syntax “<FOO>” is used to specify a coarse potential for an amino acid and a different side chain for building the full atom representation.
7. Support for D-amino acids: Chirality for D-amino acids is indicated by “&” before the coarse potential.
8. Protonation states for histidine: Support for different histidine protonation states (HIE and HID) has been added.
9. Automatic loading of affinity maps: ADCP now automatically loads affinity maps for all detected atom types in the peptide.
10. MD refinement of docked poses: Docked poses can be minimized using OpenMM, with options to control this feature.