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
Acknowledgment :
The
research presented here has been supported by Ministry of Education of the