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Street Adress:
Dr. Martin Zacharias (Professor of Theoretical Biophysics) Telephone: +49 89 289 12335 E-mail: martin.zacharias@ph.tum.de Office: Physik I, Room 2077
Christian Beier (Postdoctoral Fellow) (Room: 2073, Tel.: +4989289 12732) Srinivasaraghavan Kannan (Postdoctoral Fellow) (Room: 2059, Tel.: +4989289 13768) Piotr Setny (Postdoctoral Fellow) (Room: 2059, Tel.: +4989289 13768) Mahmut Kara (PhD student) (Room: 2073, Tel.: +4989289 12732) Simon Leis (PhD student) (Room: 2071, Tel.: +4989289 12731) Sebastian E. Schneider (PhD student) (Room: 2071, Tel.: +4989289 12731) Secretary: Former Members:
Computer simulation of biomolecular association and conformational flexibility
The Computational Biology group uses computer simulation methods to study
the structure, function and dynamics of biomolecules. Our goal is to
better understand structure formation of biomolecules and the mechanism
of ligand-receptor association. Current research areas include the
conformational analysis and structure prediction of nucleic acid motifs
and the characterisation of nucleic acid conformational flexibility.
This involves the application of molecular dynamics simulation methods
and of approaches to induce conformational deformations in biomolecules
allowing also to record associated free energy changes. The induced
conformational changes correspond for example to groove deformations of
DNA. Such deformations play a major role during the process of
protein-DNA association. The simulation studies aim at better
understanding the contribution of conformational flexibility to the
recognition process and how it is influenced by the nucleic acid
sequence. Focus of a second project is to improve computational
ligand-receptor docking approaches with an emphasis on better
accounting for conformational flexibility and biomolecule solvation.
The prediction of putative ligand binding geometries and binding sites
on a biomolecule is a major goal of bioinformatics. Most existing
approaches neglect receptor flexibility during docking. Our approaches
aim at identifying a few soft flexible degrees of freedom of a
biomolecule (e.g. domain-domain motions) and to include these during
docking. Applications include protein-small ligand interactions and
protein-protein association.
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