Competence of the organizing groups

Protein simulation and modeling, Dr André Juffer.

A simulation emulates or models on a single computer or on a collection of computers (scientific computing cluster) the behavior of a particular biological process with the objective to quantitatively measure various properties in order to gain insight into the given process. The group of Dr Juffer is experienced in such computer simulation and modeling methods (sometimes collectively called in silico modeling), and focuses on, among others, molecular dynamic simulation studies of proteins, development of coarse-grained simulation techniques, continuum electrostatics and pK_a calculations, and QM/MM studies of reaction mechanisms of enzymes. A small scale local computing cluster is available for these purposes.

Websites:

Selected papers:

S. Sharma, A. Rauk, A.H. Juffer, A DFT Study of Phosphohistidine Enzyme Intermediateon in Prostatic Acid Phosphatase. J. Amer. Chem. Soc. 130, 9708 - 9716, 2008.
W Xin and A.H.Juffer, A boundary element formulation of protein electrostatics with explicit ions. J Comput Phys, 223, 416 - 435, 2007.
S. Donnini, G Groenhof, R.K. Wierenga, A.H. Juffer, The planar conformation of a strained proline ring: a QM/MM study, Proteins, 64, 700-710, 2006.
O. Niemitalo, A. Neubauer, U. Liebal, J. Myllyharju, A.H. Juffer and P Neubauer, Modelling of translation of human protein disulfide isomerase in Escherichia coli. A case study of gene optimisation, J. Biotechnology, 120, 11-24, 2005.
S. Sharma, P. Pirila, H. Kaija, P. Vihko and A.H. Juffer, Theoretical investigations of prostatic acid phosphatase, Proteins, 58, 295 - 308, 2005.