Computational methods as a component of modern structural biology


Jaroslav Koča

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic


Computational methods and their real computer implementation have always been a part of structural biology. At the beginning, mainly computational protocols involved in experimental data refinement and interpretation in X-ray crystallography and NMR spectroscopy were used to obtain final 3-D structure.


Later on, when computers became more powerful and theoretical models more reliable, computational methods started to form an independent part of structural biology. Nowadays, computational methods are often used for, e.g., ab initio 3-D structure prediction.  One of the unique features, that make computational methods very important, is their ability to see single atoms and to follow their mutual displacement in space as a function of time.  As theoretical models are of increasing quality, computational protocols based on them are  more and more reliable and robust and, consequently, more trusted by the users. This has, besides all the good implications, also some bad effects. The key one is that the user sometimes expects to obtain more information from a computational method than such method can provide, sometimes the quality and reliability of the obtained information is overestimated.


Based mainly on research projects of the National Centre for Biomolecular Research in Brno, it  will be shown in the lecture, in which areas computational methods can successfully be used and, vice versa, where pitfalls may be expected. Examples will be given in the field of software development as well as protein complexes modeling and simulations.


Acknowledgment :


The research presented here has been supported by Ministry of Education of the Czech Republic (MSM0021622413, LC06030, ME08008) and the European Community's Seventh Framework Program under grant agreement n° 205872.