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<h2 align="center">How to use LigBuilder: PROCESS </h2>
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<p> Maybe you have noticed from the description
of GROW and LINK, the molecules generated by these two programs
will be collected in a LigBuilder LIG file. Since LigBuilder
v1.2, we have introduced a new module, PROCESS. It provides the
user the ability of analyzing a LigBuilder LIG file, extracting
the desired molecules, and converting them to viewable Mol2
files.</p>
<p> Synopsis of running PROCESS:</p>
<p> <font
color="#FF0000"><strong>process parameter_file</strong></font></p>
<p> For example:</p>
<p> process
process.index</p>
<p> The parameter file assembles all the
information necessary to run PROCESS as you wish. You should edit
the parameter file before running POCKET. The key words appeared
in this parameter file are explained as follow.</p>
<p> First, define the file needed to be
analyzed:</p>
<p> <font color="#0000FF">LIGAND_COLLECTION_FILE</font>:
The file storing the collection of molecules, in LigBuilder LIG
format. Usually it is the file specified by the key word
"LIGAND_COLLECTION_FILE" in the parameter file for GROW
or LINK. But it could also be intermediate results from GROW or
LINK.</p>
<p> Then, set up a couple of chemical criteria
for filtering out molecules. Molecules meeting all these criteria
will be considered for output. These chemical rules could be the
same as the ones you have used for GROW and LINK. But here you
can also change them to narrow your choices.</p>
<p> <font color="#0000FF">MAXIMAL_MOLECULAR_WEIGHT</font>:
The maximal molecular weight.</p>
<p> <font color="#0000FF">MINIMAL_MOLECULAR_WEIGHT</font>:
The minimal molecular weight.</p>
<p> <font color="#0000FF">MAXIMAL_LOGP</font>:
The maximal LogP.</p>
<p> <font color="#0000FF">MANIMAL_LOGP</font>:
The minimal LogP.</p>
<p> <font color="#0000FF">MAXIMAL_PKD</font>:
The maximal binding affinity to the target protein, presented in
pKd unit.</p>
<p> <font color="#0000FF">MANIMAL_PKD</font>:
The minimal binding affinity to the target protein.</p>
<p> Then, specify the outputs:</p>
<p> <font color="#0000FF">NUMBER_OF_OUTPUT_MOLECULES</font>:
Number of output molecules. Usually there are much more
candidates in the <font color="#000000">LIGAND_COLLECTION_FILE
than what you want. The program will rank all the candidates
according to their binding affinities to the target protein and
only output the top candidates. Typically 200 output molecules
are enough for idea generating.</font></p>
<p> <font color="#0000FF">SIMILARITY_CUTOFF</font>:
Maximal similarity between any two output molecules. For
instance, if it is set to 1.00, it means duplicates are not
allowed to exist. By setting this parameter, you will exert a
forced diversity on the output molecules. This parameter could be
between 0 and 1. The lower this parameter is, the higher
diversity will be achieved. We recommend this parameter to be
0.80~1.00.</p>
<p> <font color="#0000FF">OUTPUT_DIRECTORY</font>:
All the output molecules will be dumped into this directory. Each
molecule will be saved as a Mol2 file. If this directory does not
exist, the program will create it automatically. A file named
"<font color="#000000">INDEX</font>" will be created
under this directory, which lists the properties of all the
output molecules, e.g. name, molecular weight, LogP value and
binding affinity (in pKd). The program will also group all the
output molecules into different clusters according to the
similarities between them. Such information is also record in the
"INDEX" file.</p>
<p> <font color="#000000"> Running PROCESS is
not time-consuming at all. If run on a SGI O2/R10000/150M
workstation, a typical PROCESS job takes less than 10 minutes.
But we would like to remind you of two things: (1) Running the
program may take a lot of memory if the input file is really
large. Sometimes it causes memory allocation error. So if this
does happen, please edit your parameter file to narrow the ranges
of the chemical rules. (2) The running time is roughly
proportional to the size of the input file and the squared number
of output molecules. So please be careful not to set
NUMBER_OF_OUTPUT_MOLECULES too large.</font></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>
<a href="pocket.html">[POCKET]</a> <a href="grow.html">[GROW]</a>
<a href="link.html">[LINK]</a> [PROCESS] <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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