IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

LIGPLOT v.1.0 available

Andrew Wallace wallace at bsm.bioc.ucl.ac.uk
Wed Sep 14 12:28:39 EST 1994




    -------------------------------------------------------------------
    LIGPLOT: A program to generate schematic diagrams of protein-ligand
			       interactions

	       Written by Andrew Wallace and Roman Laskowski

		      University College London, UK.

    -------------------------------------------------------------------


LIGPLOT generates schematic diagrams of protein-ligand interactions
directly from the 3D coordinates of the protein and its bound ligand.

It produces clear and simple diagrams illustrating the key interactions
involved, giving an at-a-glance representation of the important atoms and
residues in both protein and ligand. Diagrams of this sort are often
presented in the literature to clarify the interactions; to show, for
example, which atoms of the ligand are hydrogen-bonded to which residues in
the protein. The diagrams are often drawn by hand and can be time-comsuming
to produce. LIGPLOT makes the process entirely automatic.

The interactions shown are those mediated by hydrogen bonds and by
hydrophobic contacts. Hydrogen-bond distances can be printed on the
bonds if required. Atom accessibilities can also be depicted, indicating
which parts of the ligand are buried and which are solvent-accessible.

In essence, the program unrolls and unfolds what can often be a complicated
3D network of interactions into a clear and simple 2D picture that gives an
at-a-glance depiction of the key interactions.

The output is a PostScript file and can be in colour as well as in
black-and-white.

Details of how to obtain the source code by anonymous ftp are presented
below.

The program is written in C, and at present is only available for unix
machines.

Three sample plots are included with the source code to give an idea of the
diagrams that can be generated:

      1. Chymotrypsin (PDB code 8gch) complexed with the tripeptide
         Gly-Ala-Trp, showing the catalytic triad of His 57, Asp 102 and
	 Ser 195 and the interactions of the ligand's Trp residue with the
	 highly hydrophobic specificity pocket in the enzyme's active site.

      2. A SH2 domain complex with a phosphotyrosine peptide (PDB code
         1sha).

      3. A `schematic peptide' diagram of an antibody-peptide complex,
         being the Fab'B1312-myohaemerythrin complex, PDB code 2igf.


IMPORTANT
---------
The inputs to the program are the PDB file to be processed and a list of
hydrogen bonds and non-bonded contacts in the structure. (The program does
not currently calculate these itself). You can generate these lists using
your own software, but we recommend using HBPLUS (written by Ian McDonald
at UCL) which many sites now have. LIGPLOT will read HBPLUS output
automatically.

If you do not have HBPLUS, you can obtain a copy from the same anonymous
ftp site as that for LIGPLOT (described below), from the directory
pub/hbplus.


Andrew Wallace       e-mail:-  wallace at bsm.bioc.ucl.ac.uk
Roman Laskowski      e-mail:-  roman at bsm.bioc.ucl.ac.uk


---------------------------------------------------------------------------

How to get LIGPLOT via anonymous ftp
------------------------------------

The anonymous ftp account can be found on: ftp 128.40.46.11

Log in as "anonymous" and enter your e-mail address as the password. (All
accesses are logged).

Once logged on, change to the pub/ligplot directory by "cd pub/ligplot".

Then retrieve two files:  "get README"
                    and:  "get ligplot.tar.Z"

Once you have quit from ftp, read the README file.

The programs are in a compressed tar file:

			 pub/ligplot/ligplot.tar.Z

You will need to uncompress the file by "uncompress ligplot.tar.Z"

Then un-tar it by "tar -xvf ligplot.tar"

The README file contains information about the documentation available
(which includes Installation Instructions) and the Confidentiality
Agreement which you will need to sign and return to us to use the programs.







More information about the Bio-soft mailing list

Send comments to us at archive@iubioarchive.bio.net