Working Group Four

Methodology development in biomolecular simulation

Working group chair – Thomas Stockner (Austria)


The shortfall in known structures relative to the database of known sequences continues to increase. However, the number of folds that proteins of typical size can adopt seems to be limited and has been estimated to be in the range of 10-15,000. Homology modeling can be used to develop models for those protein sequences for which no structure is available. This task becomes increasingly difficult with increasing sequence divergence. Simulations can provide precise predictions of possible structures and their dynamics. However, independent validation of such Molecular Dynamics (MD) predictions are essential if these computational techniques are to have a major impact and contribution to understanding of macromolecular functions. Direct comparison between simulations and experiments has proven difficult, since data are often determined on different time and size scales, and simulations typically look at patches of nanometer size for sub microsecond times. However, MD simulation times and size are now beginning to extend into ranges where direct comparison and experimental testing becomes feasible. This Working Group will be a forum for theoreticians addressing method development to interact with those who will provide experimental data that can be used to test/verify in silico predictions; substantial overlap with WG1, WG3 and WG5 should facilitate these collaborative efforts. Synergistic effects of this information exchange will also help the experimental groups gain an understanding of the various theoretical methods and their applicability.

Working group objectives 

1) Exchange of information, expertise and theoretical background of computational methods with groups in WG1/2/3/5

2) Address the limitations of current structure and complex prediction methods.

3) Develop methods and explore new possibilities for comparison between simulation and experiments.

4) Organize training and workshops for experimentalists and theoreticians

5) Presentation at international meetings and publication of results in high impact journals

WG4 will, in collaboration with WG1/2/3/5, have the following specific goals:

1) to promote parameterisation of experimental probes (spin & fluorescent) for their use in all atomic and coarse grained MD simulations.

2) to identify geometric parameters that can be extracted from experimental data and incorporated as restraints in homology modelling, docking and conformational dynamics.

3) to stimulate identification and testing of experimentally measured parameters that can be directly compared to simulations (WG1/2/3/5).

4) to promote investigations into large scale molecular motions.



Prof Bonvin Alexandre

Prof Canan Atilgan

Prof. A. Rana Atilgan

Dr. Gunnar Jeschke

Dr Christina Karatzaferi

Jens Preben Morth

Dr Tibor Páli

Dr Lubomír Rulíšek

Dr Giorgos Sakkas