Download DOCK 5 - UCSF DOCK

scoring function. The secondary scoring function is used in the final
minimization, scoring, and ranking of the molecules. If no secondary scoring
function is selected, the primary scoring function is used as the secondary.
This release contains continuous molecular mechanics based scoring
(vdw + columbic terms only), grid-based molecular mechanics scoring, contact
scoring and bump filtering as implemented in DOCK 4. Scoring grids are created
using the GRID program. DOCK also contains GB/SA scoring, as implemented
in SDOCK. Scoring grids for the GBSA code are calculated using the
accessories nchemgrid_GB and nchemgrid_SA.
This release also includes an internal energy scoring function, which is
used during the anchor & grow flexible search. This function computes the
Lennard-Jones and columbic energy between all ligand atom pairs, excluding all
1-2, 1-3, and 1-4 pairs. This energy is not included in the final reported score.
Score Optimization
Score optimization is implemented using a simplex minimizer based on
the DOCK 4 minimizer. Users can choose to minimize the rigid anchors,
minimize during flexible growth, and minimize the final conformation. The anchor
minimization is always done rigidly; also, if no flexible growth is being done, this
step will minimize the entire molecule. The minimization during the flexible
growth is a complete (torsions + rigid) minimization. The final minimization can
be rigid or torsions only, or complete. When the simplex “shrinks” enough so that
the highest and lowest points are within the scoring tolerance or if the number of
requested minimizer steps is reached, the minimizer terminates.
USING DOCK
Installing DOCK
1. Save file for appropriate operating system to hard drive.
2. Uncompress the archive into a folder called dock5/ in a directory of your
choice.
a. For windows systems, a Zip file is provided
b. For *nix systems, a gzipped archive is provided
3. All DOCK 5 binaries are installed in dock5/bin/
The dock5 directory contains the following subdirectories:
bin/