TBalius: /* Version 3.5 */

2016-04-05T15:26:04Z

Version 3.5

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	score optimization, degeneracy checking, chemical matching and critical		score optimization, degeneracy checking, chemical matching and critical
	clustering.		clustering.

			Note that this branch is still being developed and used, the latest release is [[DOCK_3.7]].

	=Version 4.0=		=Version 4.0=

Sudipto: Created page with "=Version 1.0/1.1= Authors: Robert Sheridan, Renee DesJarlais, Irwin Kuntz The program DOCK is an automatic procedure for docking a molecule into a receptor site. The recepto..."

2016-03-23T23:00:07Z

Created page with "=Version 1.0/1.1= Authors: Robert Sheridan, Renee DesJarlais, Irwin Kuntz The program DOCK is an automatic procedure for docking a molecule into a receptor site. The recepto..."

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=Version 1.0/1.1=

Authors: Robert Sheridan, Renee
DesJarlais, Irwin Kuntz

The program DOCK is an automatic procedure for
docking a molecule into a receptor site. The receptor site is
characterized by centers, which may come from sphgen or any other
source. The molecule being docked is characterized by ligand centers,
which may be its non-hydrogen atoms or volume-filling spheres
calculated in sphgen. The ligand centers and receptor centers are
matched based on comparison of ligand-center/ligand-center and
receptor-center/receptor-center distances. Sets of ligand centers match
sets of receptor centers if all the internal distances match, within a
value of distance_tolerance. Ligand-receptor pairs are added to the set
until at least nodes_minimum pairs have been found. At least three
pairs must be found to uniquely determine a rotation/translation matrix
that will orient the ligand in the receptor site. A least-squares
fitting procedure is used ([[Ferro et al. Act. Cryst. A. 1977]]).
Once an orientation has been found, it is evaluated by any of several
scoring functions. DOCK may be used to explore the binding modes of an
individual molecule, or be used to screen a database of molecules to
identify potential ligands.

=Version 2.0 =

Authors: Brian Shoichet, Dale Bodian, Irwin Kuntz

DOCK version 2.0 was written to give the user
greater control over the thoroughness of the matching procedure, and
thus over the number of orientations found and the CPU time required
([[Shoichet et al. J. Comp. Chem. 1992]]).
In addition, certain algorithmic shortcomings of earlier versions were
overcome. Versions 2.0 and higher are particularly useful for
macromolecular docking ([[Shoichet et al. J. Mol. Biol. 1991]])
and applications which demand detailed exploration of ligand binding
modes. In these cases, users are encouraged to run CLUSTER in
conjunction with sphgen and DOCK.

To allow for greater control over
searches of
orientation space, the ligand and receptor centers are pre-organized
according to their internal distances. Starting with any given center,
all the other centers are presorted into “bins”
based on
their distance to the first center. All centers are tried in turn as
“first” positions, and all the points in a bin
which has
been chosen for matching are tried sequentially. Ligand and receptor
bins are chosen for matching when they have the same distance limits
from their respective “first” points. The number of
centers
in each bin determines how many sets of points in the receptor and the
ligand will ultimately be compared. In general, the wider the bins, the
greater the number of orientations generated. Thus, the thoroughness of
the search is under user control.

=Version 3.0=

Authors: Elaine Meng, Brian Shoichet,
Irwin Kuntz

Version 3.0 retained the matching
features of version 2.0, and introduced options for scoring
([[Meng et al. J. Comp. Chem., 1992]]).
Besides the simple contact scores mentioned above, one can also obtain
molecular mechanics interaction energies using grid files calculated by
CHEMGRID (which is now superseded by GRID in version 4.0). More
information about the ligand and receptor molecules is required to
perform these higher-level kinds of scoring. Point charges on the
receptor and ligand atoms are needed for electrostatic scoring, and
atom-type information is needed for the van der Waals portion of the
force field score. Input formats (some of them new in version 3.5) are
discussed in various parts of the documentation; one example of a
“complete format” (including point charges and atom
type
information) is SYBYL MOL2 format. Parameterization of the receptor is
discussed in the documentation for CHEMGRID. In DOCK, ligand parameters
are read in along with the coordinates; input formats are described
below. Currently, the options are: contact scoring only, contact
scoring plus Delphi electrostatic scoring, and contact scoring plus
force field scoring. Atom-type information and point charges are not
required for contact scoring only.

=Version 3.5 =

Authors: Mike Connolly, Daniel
Gschwend, Andy Good, Connie Oshiro, Irwin Kuntz

Version 3.5 added several features:
score optimization, degeneracy checking, chemical matching and critical
clustering.

=Version 4.0=

Authors: Todd Ewing, Irwin Kuntz

Version 4.0 was a major rewrite and update of DOCK
([[Ewing et al. 2001]]).
A new matching engine was developed which is more robust, efficient,
and easier to use ([[Ewing and Kuntz. J. Comput. Chem. 1997]]).
Orientational sampling can now be controlled directly by specifying the
number of desired orientations. Additional features include chemical
scoring, chemical screening, and ligand flexibility.

=Version 5.0-5.4=

Authors: Demetri Moustakas, P. Therese
Lang, Scott Pegg, Scott Brozell, Irwin Kuntz

Version 5 was rewritten in C++ in a modular format,
which allows for easy implementation of new scoring functions, sampling
methods and analysis tools ([[Moustakas et al., 2006]]).
Additional new features include MPI parallelization, exhaustive
orientation searching, improved conformation searching, GB/SA solvation
scoring, and post-screening pose clustering.
([[Zou et al. J. Am. Chem. Soc., 1999]])

=Version 6.0-6.8=

DOCK 6 is an extension of the DOCK 5 code base. It
includes the implementation of Hawkins-Cramer-Truhlar GB/SA solvation
scoring with salt screening and PB/SA solvation scoring through
OpenEye's Zap Library. Additional flexibility has been added to scoring
options during minimization. The new code also incorporates DOCK
version 3.5.54 scoring features like Delphi electrostatics,
ligand desolvation, and receptor
desolvation. Finally, DOCK 6 introduces new code that allows access to
the NAB library of functions such as receptor flexibility, the full
AMBER molecular mechanics scoring function with implicit solvent,
conjugate gradient minimization, and molecular dynamics simulation
capabilities.
See [[Lang et al. RNA, 2009]],[[Brozell et al., 2012]] [[Allen et al., 2015]], and [[Jiang et al., 2015]].

History of DOCK 6 - Revision history

TBalius: /* Version 3.5 */

Sudipto: Created page with "=Version 1.0/1.1= Authors: Robert Sheridan, Renee DesJarlais, Irwin Kuntz The program DOCK is an automatic procedure for docking a molecule into a receptor site. The recepto..."