DOCK is a separate program that calculates possible binding orientations, given the structures of ligand and receptor molecules. Some uses are to examine a particular binding interaction or to search a database for ligands of a target receptor.
Dock Prep can perform several tasks to prepare structures as input to the DOCK suite of programs (or for other types of calculations):
If there are extra molecules other than solvent that should not be present during docking, these should be deleted before Dock Prep is run. Dock Prep does not delete extra chains or other molecules besides solvent, because depending on the specific situation, they might be important for binding or maintaining receptor structure. Similarly, binding might require the presence of more chains than are included in the structure file; the relevant form should be generated before Dock Prep is run (see also Unit Cell).
There are several ways to start Dock Prep, a tool in the Structure Editing category (including using it via Minimize Structure).
Under Molecules to prep, the structure(s) of interest should be chosen from the list of open molecule models. Individual models or blocks of models can be chosen with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.
Several operations can be performed on the chosen structures:
An alternative approach is to repair truncated sidechains with swapaa beforehand.
After AddH is done, Dock Prep re-examines chain-terminal residues and adjusts their charge states as needed. Residues at the ends of connected chains are inspected to determine whether they are real termini, based on any SEQRES information in the input PDB file (or the mmCIF equivalent) and the presence or absence of additional chains with the same IDs. Real N-termini are assumed to be positively charged (+H3N–) and real C-termini are assumed to be negatively charged (–CO2–). If a C-terminal carboxylate is missing an oxygen (OXT), it will be added. End residues that are not real termini are terminated like other chain-internal residues, with N(H)– and –C(=O). The position of the N-end "amide" hydrogen in such cases is not fully determined by the positions of the existing atoms; Dock Prep places this hydrogen to produce a φ angle equal to that of the subsequent residue.
Charges for standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are looked up using assignment files based on the Amber parameter files all*94.lib. If any atoms in standard residues are not recognized, a warning will appear and information on the atoms will be sent to the Reply Log. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved.
Charges for nonstandard residues, if any, are calculated using Amber's Antechamber module (included with Chimera; publications involving its use should cite the reference). It is necessary to specify the formal charge of each nonstandard residue and which charge calculation method should be used.
Tasks are performed in the order listed on the Dock Prep dialog. If any individual step is canceled, subsequent steps will not be performed; for example, if charge assignment is canceled, a Mol2 file will not be written. To skip a particular step, uncheck its option before initiating the Dock Prep calculation.
A related tool is ViewDock, which facilitates interactive screening of DOCK output.
Does not build missing residues or truncated sidechains. Structures may have missing residues or atoms where coordinates could not be determined, often due to disorder or flexibility. Dock Prep does not build in any missing residues or truncated sidechains. C-terminal OXT atoms are the only heavy (nonhydrogen) atoms that will be added when missing from a structure. Residues with truncated sidechains can be mutated to alanine or glycine depending on whether CB atoms are present.