{"id":14,"date":"2018-12-14T00:43:17","date_gmt":"2018-12-14T00:43:17","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/ccsb-3\/?page_id=14"},"modified":"2025-01-16T16:57:30","modified_gmt":"2025-01-16T16:57:30","slug":"autodock-crankpep","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adcpv11\/","title":{"rendered":"Homepage"},"content":{"rendered":"

AutoDock CrankPep v1.1<\/h1><\/h1><\/div>

The older and deprecated version of ADCP (Version 1.0) is available here<\/a><\/p>\n<\/div>

AutoDock CrankPep is part of the AutoDock Suite<\/a>.<\/p>\n<\/div>

<\/div><\/div><\/div>

AutoDock CrankPep<\/strong><\/em> (ADCP<\/strong><\/em>) 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.<\/p>\n

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:<\/p>\n

    \n
  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.<\/li>\n
  2. Improved representation: Docked poses now include all-atom side chain representations, rather than a rotamer index.<\/li>\n
  3. User-defined number of docked poses: Users can set the number of docked poses using the “-m” or “–nmodes” command line option.<\/li>\n
  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.<\/li>\n
  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.<\/li>\n
  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.<\/li>\n
  7. Support for D-amino acids: Chirality for D-amino acids is indicated by “&” before the coarse potential.<\/li>\n
  8. Protonation states for histidine: Support for different histidine protonation states (HIE and HID) has been added.<\/li>\n
  9. Automatic loading of affinity maps: ADCP now automatically loads affinity maps for all detected atom types in the peptide.<\/li>\n
  10. MD refinement of docked poses: Docked poses can be minimized using OpenMM, with options to control this feature.<\/li>\n<\/ol>\n

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