📄 pocket.html
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<h2 align="center">How to use LigBuilder: POCKET </h2>
<hr>
<p> POCKET has two main functions: first,
analyze the binding pocket and prepare the information necessary
for running GROW or LINK; second, derive the key interaction
sites within the binding pocket and suggest a pharmacophore
model. Such a model could be applied to 3D database searching.</p>
<p> Synopsis of running POCKET:</p>
<p> <font
color="#FF0000"><strong>pocket parameter_file</strong></font></p>
<p> For example:</p>
<p> pocket
pocket.index</p>
<p> The parameter file assembles all the
information necessary to run POCKET as you wish. You should edit
the parameter file before running POCKET. The key words appeared
in this parameter file are explained in the following.</p>
<p> First, tell the program about the inputs :</p>
<p> <font color="#0000FF">RECEPTOR_FILE</font>:
The PDB file presenting the target protein. This file is
absolutely necessary to run POCKET. We suggest that the 3D
structure of the target protein comes from a complex rather than
an unbound one. Waters and metal ions may be left to the protein
in this file if you want them to be considered. Any other small
molecule, such as ligand, cofactor, and counter ion, should be
eliminated.</p>
<p> <font color="#0000FF">LIGAND_FILE</font>:
The Mol2 file presenting a ligand of the target protein. It helps
POCKET to define where the binding pocket locates. Therefore it
will be ideal if the size, shape, and location of the ligand is
proper. This is not demanding: a ligand extracted directly from
the complex structure will be just fine.</p>
<p> <font color="#0000FF">PARAMETER_DIRECTORY</font>:
The path of the directory "<font color="#0000FF">parameter</font>".
Under this directory, there are force field parameters used by
LigBuilder. Parameters for atoms, bonds, and torsions are all
cited from Tripos force field. This directory is used by POCKET,
GROW, LINK, and PROCESS.</p>
<p> Then, define the outputs, which will be
utilized by GROW or LINK later:</p>
<p> <font color="#0000FF">POCKET_ATOM_FILE</font>:
The output file listing the atoms forming the binding pocket. It
is in plain text. </p>
<p> <font color="#0000FF">POCKET_GRID_FILE</font>:
The output file listing the grids inside the binding pocket. It
is in plain text.</p>
<p> As mentioned above, POCKET also has an
interesting feature: it will derive the key interaction sites
inside the binding pocket and, based on that, suggest a
pharmacophore model. The following items are concerned with this:</p>
<p> <font color="#0000FF">KEY_SITE_FILE</font>:
The output file storing the key interaction sites derived inside
the binding pocket. It is in PDB format, in which nitrogen atoms
(blue) represent hydrogen-bond donor sites; oxygen atoms (red)
represent hydrogen-bond acceptor sites; and carbon atoms (green)
represent hydrophobic sites. You can use any molecular modeling
software to view this file and obtain an insight into the
characteristics of the binding pocket. </p>
<p align="center"><img src="key_site.gif"
alt="key_site.gif (9487 bytes)" width="417" height="238"></p>
<p align="center"><font color="#0000A0">Example of the key
interaction sites<br>
(Phospholipase A2, PDB entry 1POE)</font></p>
<p> <font color="#0000FF">PHARMACOPHORE_PDB_FILE</font>:
The output file storing the derived pharmacophore model. It is in
PDB format. The definition of key features is the same as the one
in <font color="#000000">KEY_SITE_FILE.</font></p>
<p align="center"><img src="pharmacophore.gif"
alt="pharmacophore.gif (11243 bytes)" width="389" height="241"></p>
<p align="center"><font color="#0000A0">Example of the derived
pharmacophore model<br>
(Phospholipase A2, PDB entry 1POE)</font></p>
<p> <font color="#0000FF">PHARMACOPHORE_TXT_FILE</font>:
The output file storing the information of the derived
pharmacophore model. It lists the pharmacophore features and the
internal distances between them. It also ranks all the features
according to their binding scores. Actually, it is the text
version of <font color="#000000">PHARMACOPHORE_PDB_FILE</font>.</p>
<p> <font color="#0000FF">MINIMAL_FEATURE_DISTANCE</font>:
This parameter sets the minimal distance between any two
pharmacophore features. It is in Angstrom. We recommend that it
should not be less than 3.00. </p>
<p> <font color="#0000FF">MAXIMAL_FEATURE_NUMBER</font>:
This parameter sets the maximal number of pharmacophore features
which will be included in the final model. To get a meaningful
pharmacophore model, this number should not be either too large
or too small. We recommend that it should be between 3 and 8.</p>
<p> <font color="#000000">Please notice:</font>
LigBuilder adopts the "rigid receptor" assumption.
Therefore, for a given target protein, you just need to run
POCKET only once. That means you do not have to run POCKET each
time before you want to run GROW or LINK.</p>
<p> POCKET is fast. If run on a SGI
O2/R10000/150M workstation, a typical POCKET job takes only a few
minutes. The running time will increase a little if the size of
the binding pocket is larger than the average.</p>
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<p align="center"><a href="index.html">[Content]</a> <a
href="intro.html">[Introduction]</a> <a href="download.html">[Download]</a>
<a href="install.html">[Install]</a> <a href="overview.html">[Overview]</a>
[POCKET] <a href="grow.html">[GROW]</a> <a href="link.html">[LINK]</a>
<a href="process.html">[PROCESS]</a> <a href="skill.html">[Skills]</a>
<a href="faq.html">[FAQs]</a></p>
<p align="center"><font size="2"><em>(These web pages are edited
by Dr. Renxiao Wang. Latest update: August, 2000)</em></font></p>
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