Nucleic Acids Research, 2003, Vol. 31, No. 13 3356-3358
© 2003 Oxford University Press
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
A. S. Z. Hussain,
Ch. Kiran Kumar,
C. K. Rajesh,
S. S. Sheik and
K. Sekar*
Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560 012, India
*To whom correspondence should be addressed. Tel: +91 803601409; Fax: +91 803600683; Email: sekar{at}physics.iisc.ernet.in
Received December 30, 2002; Revised and Accepted April 9, 2003
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ABSTRACT
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SEM, Symmetry Equivalent Molecules, is a web-based graphical
user interface to generate and visualize the symmetry equivalent
molecules (proteins and nucleic acids). In addition, the program
allows the users to save the three-dimensional atomic coordinates
of the symmetry equivalent molecules in the local machine. The
widely recognized graphics program RasMol has been deployed
to visualize the reference (input atomic coordinates) and the
symmetry equivalent molecules. This program is written using
CGI/Perl scripts and has been interfaced with all the three-dimensional
structures (solved using X-ray crystallography) available in
the Protein Data Bank. The program, SEM, can be accessed over
the World Wide Web interface at
http://dicsoft2.physics.iisc.ernet.in/sem/ or
http://144.16.71.11/sem/.
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INTRODUCTION
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In the present structural Bioinformatics era, advanced tools
are highly essential to facilitate the display of useful information
from the wealth of data available in the public repository Protein
Data Bank (PDB) (
1). The PDB is an archive of three-dimensional
biological macromolecular structures determined experimentally
using well-known techniques such as X-ray crystallography and
NMR spectroscopy and is maintained by the Research Collaboratory
for Structural Bioinformatics (RCSB). The three-dimensional
structures are constantly being used by many researchers all
over the world to unravel the underlying structure–function
relationships. Towards this effort, several crystallographic
modeling packages such as FRODO (
2), CHAIN (
3), ‘O’
(
4) and SETOR (
5) are available to generate and visualize the
macromolecules (determined using the well known physical technique
of X-ray crystallography) and its symmetry equivalent molecules.
Almost all these programs have much less control to visualize
the symmetry equivalent molecule(s) corresponding to a particular
equivalent position present in the space group. Again, it is
often difficult to save the three-dimensional atomic coordinates
of the user interested symmetry equivalent molecules in the
local machine for further analysis. To the best of our knowledge,
there is no web-based program available to perform the above
operations on all the crystal structures available in the PDB
(
1). To overcome this lacuna, with the least human intervention,
the program SEM has been developed with the following features.
- Symmetry related molecules around the reference molecule.
- Molecules within the unit cell.
- Molecules outside the unit cell.
- Molecules within and outside the unit cell.
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USAGE OF THE SOFTWARE
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Towards this end, an efficient methodology has been designed
(Fig.
1) to generate all the molecules within and outside the
unit cell around the reference molecule. In addition, a graphics
display facility has been provided to visualize the molecules
and separate colour schemes have been adopted for the convenience
of the users. The user needs to supply the following information
associated with the given molecule in the appropriate box provided
in the web page: for the three-dimensional crystal structures,
available in the PDB (
1), the user needs to provide the four
character PDB-id code. The necessary values (unit cell constants
and space group) will be automatically taken by the program
from the uploaded atomic coordinate file. In addition, the user
needs to choose the space group information from the pull down
menu. The three-dimensional atomic coordinates of all the structures
are available at the locally maintained anonymous PDB-FTP server,
Bioinformatics Centre, Indian Institute of Science, Bangalore,
India. The user needs to provide the following for the structures
uploaded from the client machine: (i) upload the three-dimensional
atomic coordinates in the PDB (
1) format through the web browser;
(ii) enter the unit cell constants (in Å units) and
,
ß and
(in degrees) in the box provided; and (iii)
choose the space group from the pull down menu box. The symmetry
equivalent points for all the space groups have been incorporated
in the program and the user needs to choose the correct space
group using the pull down menu to get the corresponding equivalent
positions from the in-built database.
The software is very flexible and has the option of visualizing
all the symmetry equivalent molecules or any particular molecule
generated within the unit cell. In addition, the user can save
the three-dimensional atomic coordinates of all or any particular
molecule(s) in the unit cell into their local hard disk. To
perform this, the user needs to click ‘Click here to visualize
the structures’ and then use the colour scheme provided
in the pop-up window. Using the colour scheme, the user can
choose a particular model or a set of models whose three-dimensional
structure is to be viewed or to be saved in the local machine.
In addition, the program has an option to highlight a particular region of the molecule (in different representations) in the reference and its symmetry equivalent molecules. In this way, the users can see the role of a particular fragment in the crystal packing. The public domain graphics program RasMol (6) has been deployed and incorporated with the proposed package to visualize the reference and the symmetry related molecule(s). The user needs to interface the graphics program, RasMol, with the Netscape browser (only for the first time) (for instructions: http://144.16.71.11/sem/rasconf.html/). The program SEM is self-explanatory, easy to use and tested on Windows 95/98/2000, Windows NT, Linux and SGI platforms through the most popular WWW (World Wide Web) browser Netscape. The program is completely general and will work for most of the space groups available in the International Tables. The program can be used to see how the molecules are packed and arranged in the unit cell with respect to the reference molecule. In addition, this package can be used to generate the active biological tetramer from the two-homo dimers (7) like the protein quaternary structure (PQS) file server (8), which is an internet resource specially designed to generate the quaternary assembly. At the general outset, the package SEM is a very good teaching tool to the students undergoing graduate programs in structural Bioinformatics and X-ray crystallography. The symmetry related molecules of the protein structure (9) (PDB-id code: 1UNE
[PDB]
) generated using this program is shown in Figure 2.
View larger version (58K):
[in this window]
[in a new window]
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Figure 2. This page depicts the typical output of the program SEM for the PDB-id code: 1UNE
[PDB]
(9). Few symmetry equivalent molecules (see checked boxes in the left panel) (backbone representation with different colours) along with the reference molecule (white colour ribbon representation) are shown. Each coloured molecule belongs to a particular symmetry equivalent position (see left side panel for colouring schemes and other details).
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The program SEM is written using CGI/Perl scripts and can be
executed on our Bioinformatics Linux server [a 3.06 GHz
Pentium IV processor; 1Gb (RD-RAM) of main memory]. The input
data part and the pull down menu of this program are written
in HTML and Java scripts. All the three-dimensional structures
(using the most popular technique, X-ray diffraction) available
in the PDB (
1) have been incorporated in this package. The atomic
coordinates are being updated every week and made available
locally in our PDB-FTP server (Bioinformatics Centre, Indian
Institute of Science, Bangalore, India). Hence, the users can
access all the crystal structures available in the PDB at any
given time. In the trial runs, the results appeared in about
30–40 s depending upon the size of the protein molecule
and the network traffic. Please send your comments and suggestions
for the inclusion of additional options to Dr K. Sekar (
sekar{at}physics.iisc.ernet.in).
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ACKNOWLEDGEMENTS
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The authors gratefully acknowledge the use of the Bioinfomatics
Centre (DIC), the Interactive Graphics Based Molecular Modeling
(IGBMM) and the Supercomputer Education and Research Centre
(SERC). The facilities DIC and IGBMM are supported by the Department
of Biotechnology (DBT), Government of India.
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REFERENCES
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- Jones,T.A. (1985) FRODO: diffraction methods for biological macromolecules. Interactive Graphics: FRODO. Methods Enzymol., 115, 157–191.[ISI][Medline]
- Sack,J. and Quiocho,F.A. (1992) CHAIN: Crystallographic Modelling Program. Baylor College of Medicine, Houston, TX.
- Kleywegt,G.J., Zou,J.Y., Kjeldgaard,M. and Jones,T.A. (2001) ‘Around O’, In Rossmann,M.G. and Arnold,E. (eds), International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules. Kluwer Academic Publishers, Dordrecht, The Netherlands, Chapter 17.1, pp. 353–356, 366–367.
- Evans,S.V. (1993) SETOR: hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph., 11, 134–138.[CrossRef][ISI][Medline]
- Sayle,R.A. and Milner-Whilte,E.J. (1995) RASMOL: Biomolecular graphics for all. Trends Biochem. Sci., 20, 374–382.[CrossRef][ISI][Medline]
- Sankaranarayanan,R., Sekar,K., Banerjee,R., Sharma,V., Surolia,A. and Vijayan,M. (1996) A novel mode of carbohydrate recognition in Jacalin, a Moraceae plant lectin with a ß-prism fold. Nature Struct. Biol., 3, 596–602.[CrossRef][ISI][Medline]
- Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358–361.[CrossRef][ISI][Medline]
- Sekar,K. and Sundaralingam,M. (1999) High resolution refinement of orthorhombic bovine pancreatic phospholipase A2. Acta Cryst., D55, 46–50.
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