Molecular systems biology: Molecular simulations of proteins and their complexes

R. Ettrich¹

¹Laboratory of High Performance Computing, Institute of Systems Biology and Ecology ASCR and Institute of Physical Biology USB, Zámek 136, CZ-373 33 Nové Hrady, Czech Republic.

Email: ettrich@greentech.cz

Simulationon a molecular level has evolved to become the tool of choice to model the physical properties of complex biological systems. Molecular dynamics simulations as such have become the “workhorse” of structural biologists. Ten years ago state of the art simulations could barely access the nanosecond time scale and the increase in cpu power has pushed this limit two orders of magnitude. Interestingly, the increase in power of simulations is only partly due to the large increase in computing power during the past 50 years. Development of novel computational techniques extend molecular simulations towards longer time and length scales in molecular systems biology. Three-dimensional structures to build up a stable complex biological system that might be studied by means of molecular dynamics are gained either by experimental techniques of X-ray diffraction and protein NMR or by homology and energetic modeling in combination with low-resolution spectroscopic techniques as are circular dichroism, Raman spectroscopy or FTIR.

This research was supported by the Ministry of Education, Youth and Sports of the Czech Republic (MSM6007665808, LC06010) and by the Academy of Sciences of the Czech Republic (Institutional research concept AVOZ60870520)