Structural Bioinformatics - a Bridge between Structural
Biology and Bioinformatics
J. Koča1,2, R. Svobodová Vařeková 1,2, D. Sehnal 1,2,, C.-M. Ionescu1, S. Geidl1,2,
L. Pravda1,2, D. Jaiswal1, V. Horský 2, M. Wimmerová 1,2
1CEITEC - Central European Institute of
Technology, Masaryk University, Brno, Czech Republic
2National Centre for Biomolecular Research, Faculty of Science, Masaryk
University, Brno, Czech Republic
Structural biology of today is a well-defined
field of science. It is not so for bioinformatics, which is understood from
very narrow classical view (informatics of the genome) on the one hand, to very
wide concept of informatics of any biology related information. In all cases,
bioinformatics becomes an important field of science as the amount of bio-related
information, especially from Next Generation Sequencing (NGS), is increasing
dramatically, and, for the time being, there is no software tool available that
would be able to extract all the biological information hidden in the data.
In contrary, structural bioinformatics is relatively
well defined part of bioinformatics (see, for example1-2), which is
related to the analysis and prediction of the three-dimensional structure of
biological macromolecules.The term structural has the same meaning as in
structural biology, and structural bioinformatics
can be seen as a part of computational structural biology. Even if the grow
of 3D structural data is much lower compared to NGS, also here the increase is
exponential and calls for new approaches to extract structurally and/or biologically
relevant information.
In our group, we have developed several
software tools that are able to help in solving such a task. These are
MotiveQuery3 for quick finding and extraction of biomacromolecular
fragments, SiteBinder4 for fast and accurate comparison of these
fragments, MotiveValidator5 and ValidatorDB6 for
validation of ligands and non-standard residues, and AtomicChargeCalculator7
for calculation of partial atomic charges. Last but not least, we have developed
also MOLE8, a software tool for detection and characterization of
channels and pores in biomacromolecules. All the software tools are accessible
from the link http://ncbr.muni.cz/WebChemistry
1. Bourne, P.E., and Gu, J. (2009) Structural
Bioinformatics (2nd edition), John Wiley & Sons, New York, ISBN
978-0-470-18105-8
2. Bourne, P.E., and Weissig, H. (2003) Structural
Bioinformatics, Wiley ISBN 0-471-20199-5
3. Sehnal, D., Pravda, L., Svobodová Vařeková, R.,
Ionescu, C.-M., and Koča, J.: MotiveQuery: Web application for fast detection
of biomacromolecular fragments in whole Protein Data Bank. (prepared for
submission)
4. Sehnal, D., Svobodová Vařeková, R., Huber, H. J., Geidl, S., Ionescu, C. M., Wimmerová, M., and Koča,
J. SiteBinder: An improved approach for comparing multiple protein structural
motifs. J. Chem. Inf. Model. (2012), 52(2), 343–359.
5. Svobodová Vařeková, R., Jaiswal, D., Sehnal,
D., Ionescu, C.-M., Geidl, S., Pravda, L., Horský, V., Wimmerová, M., and Koča,
J.: MotiveValidator: interactive web-based validation of ligand and residue
structure in biomolecular complexes. Nucleic Acids Res. (2014), 42, W227-33.
6. Sehnal D., Svobodová Vařeková R., Pravda L.,
Ionescu C.-M., Geidl S., Horský V., Jaiswal D., Wimmerová M., and Koča J.:
ValidatorDB – database of up-to-date and comprehensive validation results for
ligands and non-standard residues from the Protein Data Bank. Nucleic Acids
Res. (2014), 43(D1), D369–D375.
7. Ionescu, C.-M., Sehnal, D., Svobodová Vařeková,
R., Geidl, S., Falginella, F.L., Pant, P., Pravda, L., Mishra, S.K., and
Koča, J.: AtomicChargeCalculator: Interactive Web-based calculation of atomic
charges in large biomolecular complexes and drug like molecules (prepared for
submission)
8. Berka, K., Hanák, O., Sehnal, D., Banáš, P.,
Navrátilová, V., Jaiswal, D., Ionescu, C.-M., Svobodová Vařeková, R., Koča, J.,
and Otyepka, M. MOLEonline 2.0: interactive web-based analysis of biomacromolecular
channels. Nucleic Acids Res. (2012), 40(W1), W222–W227.