Structural Bioinformatics - a Bridge between Structural Biology and Bioinformatics

J. Koča^1,2, R. Svobodová Vařeková ^1,2, D. Sehnal ^1,2,, C.-M. Ionescu¹, S. Geidl^1,2, L. Pravda^1,2, 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 example^1-2), 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.