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<title>User manual for LigBuilder v1.2</title>
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<h2>
How to use LigBuilder: An overview</h2></center>
<hr>
<ol>
<li>
<a href="#subject_1">Growing strategy and linking strategy</a></li>
<li>
<a href="#subject_2">Overall structure of LigBuilder</a></li>
<li>
<a href="#subject_3">Examples for learning LigBuilder</a></li>
</ol>
<hr>
<h4>
<a NAME="subject_1"></a><font color="#0000FF">1. Growing strategy and linking
strategy</font></h4>
The central function of LigBuilder is constructing ligand
molecules within the constraints of the target protein. As mentioned in
the <a href="intro.html">Introduction</a> section, LigBuilder supports
two strategies to do this, i.e. <font color="#0000FF">growing strategy</font>
and <font color="#0000FF">linking strategy</font>. To apply the growing
strategy, you need to provide a pre-placed "<font color="#0000FF">seed</font>"
structure inside the binding pocket and LigBuilder will subsequently add
fragments onto it to build molecules. This strategy may be helpful when
you have got an interesting lead compound and want to develop its derivatives
to improve the bioactivity (<font color="#000000">lead optimization</font>).
To apply the linking strategy, you also need to provide a starting structure,
which consists of several separated chemical fragments. These fragments
should be pre-placed inside the binding pocket and would better to form
favorable interactions with the target protein. Then LigBuilder will try
to build molecular frameworks to link those fragments into integrated molecules.
This strategy may be helpful when you try to find novel lead compounds
(<font color="#000000">lead discovery</font>).
<center>
<p><img SRC="strategy.gif" ALT="strategy.gif (8296 bytes)" height=321 width=354>
<p><font color="#0000A0">Illustration of growing strategy and linking strategy</font></center>
<hr>
<h4>
<a NAME="subject_2"></a><font color="#0000FF">2. Overall structure of LigBuilder</font></h4>
LigBuilder has four main functional modules, i.e. POCKET,
GROW, LINK, and PROCESS. POCKET is designed to analyze the binding pocket
of the given protein and prepare the data necessary to run GROW or LINK.
GROW is designed for performing growing strategy while LINK for linking
strategy. The ligands generated by GROW or LINK will be collected in a
data file and read by PROCESS to give the final viewable results.
<center>
<p><img SRC="ligbuilder.gif" height=236 width=436>
<p><font color="#0000A0">An overview of LigBuilder program</font></center>
<p> In short, if you have chosen growing strategy, run
POCKET then GROW then PROCESS; Or if you have chosen linking strategy,
run POCKET then LINK then PROCESS.
<p> All of the four modules of LigBuilder, i.e. POCKET,
GROW, LINK, and PROCESS, have the uniform synopsis to run (you do not have
to remember a lot of weird stuffs!):
<p> <font color="#FF0000">pocket
parameter_file_for_POCKET</font>
<p> <font color="#FF0000">grow
parameter_file_for_GROW</font>
<p> <font color="#FF0000">link
parameter_file_for_LINK</font>
<p> <font color="#FF0000">process
parameter_file_for_PROCESS</font>
<p> The parameter file defines the input files, the output
files, and all the necessary parameters to run the program as you wish.
It is in plain text, in which each line starts with a key word. You can
find the detailed explanation of all the key words in the following pages
of this manual.
<br>
<hr>
<h4>
<a NAME="subject_3"></a><font color="#0000FF">3. Examples for learning
LigBuilder</font></h4>
We have provided some example files for you to practise
using LigBuilder. You can find two samples in the directory "<font color="#0000FF">example</font>":
<p> (1) Alpha-Thrombin (PDB entry 1DWD):
<p><font face="Courier"><font size=-1> 1dwd.pdb
PDB file of the protein (for POCKET)</font></font>
<br><font face="Courier"><font size=-1> 1dwd.mol2
Mol2 file of the ligand (for POCKET)</font></font>
<br><font face="Courier"><font size=-1> 1dwd_grow.mol2
Mol2 file of the seed structure (for GROW)</font></font>
<br><font face="Courier"><font size=-1> 1dwd_link.mol2
Mol2 file of the seed structure (for LINK)</font></font>
<p> (2) Dihydrofolate Reductase (PDB entry 4DFR):
<p><font face="Courier"><font size=-1> 4dfr.pdb
PDB file of the protein (for POCKET)</font></font>
<br><font face="Courier"><font size=-1> 4dfr.mol2
Mol2 file of the ligand (for POCKET)</font></font>
<br><font face="Courier"><font size=-1> 4dfr_grow.mol2
Mol2 file of the seed structure (for GROW)</font></font>
<br><font face="Courier"><font size=-1> 4dfr_link.mol2
Mol2 file of the seed structure (for LINK)</font></font>
<p> Sample parameter files, i.e. "<font color="#0000FF">pocket.index</font>",
"<font color="#0000FF">grow.index</font>", "<font color="#0000FF">link.index</font>",
and "<font color="#0000FF">process.index</font>", are also included in
the same directory.
<br>
<hr>
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<p><a href="index.html">[Content]</a> <a href="intro.html">[Introduction]</a><a href="download.html">[Download]</a>
[<a href="install.html">Install</a>] [Overview] <a href="pocket.html">[POCKET]</a>
<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><i><font size=-1>(These web pages are edited by Dr. Renxiao Wang. Latest
update: August, 2000)</font></i></center>
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