DOCK search procedure

Desmet et al. (291) used a truncated (deadend elimination) search procedure to bind flexible peptides to the MHC I receptor. The translation/rotational space covered 6636 relative orientations and each nonglycine/proline residue of the peptide had 47 main-chain con-formers. Side chains had threefold rotations about their chi angles and 28 side chains of the receptor were allowed to rotate. Seventy-four low energy structures were obtained with an average rmsd of 1 A. The lowest energy structure had an rmsd of 0.56 A. Peptides up to 20 residues were docked with this procedure. 

The two similarity searching procedures discussed thus far in this section make no attempt to align the target molecule with each of the database structures the elimination of this step is one of the main reasons why these programs are so fast in operation. The remaining procedures, called DOCK, CLIX, and SPERM, all consider the precise alignment of the target structure in the calculation of similarity. 

Another method of systematic search is the use of databases of pregenerated conformations. Conformations are calculated once and the search problem is reduced to a rigid body docking procedure. This is the main concept of FLOG docking program. ... 

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