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Molecular DataSpace
Molecular Data Space is a web application that accesses one or more servers
to request the
3-D coordinates and information of protein structures and small organic
drug compounds. The
retrieved structures can then be visualized using a graphics
program like Rasmol or a
web based graphics program like Webmol. Also the 3-D structures of the
molecules can be displayed in
CML and PDB file formats. Most importantly a distributed query can be done
between a protein
molecule and a small organic compound. One such query that might be done
to understand how
a drug candidate interacts with protein structures using a docking algorithm.
Molecular DataSpace contains atomic coordinates and descriptions of protein
structures and small organic
compounds. Protein structural data and some of the organic compounds were
obtained from the
Protein Data Bank (PDB) at the Research Collaboratory for Structural
Bioinformatics (RCSB)[1]. The atomic coordinates
for the rest of the organic compounds were obtained from the Molecular Models from Chemistry at Okanagan University College.
The entire data set is being maintained and served over the internet using
the Data Space Transfer Protocol (DSTP)
developed at the National Center for Data Mining at the University of
Illinois at Chicago (UIC).
The entire protein and drug data can be browsed or a search tool can be used to retrieve protein structures
based on a particular criteria. The data can be searched by one or more
PDB identification codes (PDB ID);
by searching the text found in the description of the protein, like hiv or homo sapiens; or by
searching the name of one of the authors of the protein structure.
After the desired structures have been retrieved several queries can be done on them using different tools.
The 3-D structures can be viewed in Chemical Markup Language (CML)
format. Also the 3-D structures can be visualized using Rasmol, a wildly available graphics program, or
directly over the web using Webmol[2].
Information associated with each structure can also be accessed.
In order to use Rasmol one has to dowmload the executable of the graphics package for the desired
operating system from the home page and link it to the
extension .xyz on one's web browser.
Alternatively, the 3-D graphics can be viewed directly over the web using WebMol option and several queries
can be done on a particular structure. Some of these queries include distance and angle measurements,
interactive distance matrix plot, interactive Ramachandran plot, detection of cavities, and numerical
calculation of solvent accesible surface, van der Waals surface and volume.
Finally, one can predict the structure of a complex by using the Global Range Molecular Matching (GRAMM)[3]
algorithm (a docking algorithm). The algorithm can be executed by selecting two structures. The program will
output one or several possible orientations of the complex that can be viewed using WebMol.
- H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000)
- Walther D. WebMol - a Java based PDB viewer. Trends Biochem Sci, 22 pp. 274-275 (1997)
- E. Katchalski, L. Shariv, M. Eisenstein, A. A. Friesem, C. Aflalo, L. A. Vakser, Molecular surface
recongnition: Determination of geometric fit between proteins and their lignands by correlation techniques.
Proc. Natl. Acad. Sci. USA,, 89 pp. 2195-2199 (1992)
Shirley Connelly
Last modified: Thu Oct 25 15:08:39 CDT 2001
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