Coarse-Grained Models to Simulate Dynamics of Biomolecules
Professor Joanna Trylska
Centre of New Technologies, University of Warsaw, Poland
ABSTRACT
Biomolecules are inherently flexible and their dynamics affects
ligand binding. To investigate the internal dynamics of proteins
and nucleic acids, we apply all-atom molecular dynamics
simulations. However, atomistic level of detail makes simulations
too computationally demanding to describe folding and global
motions so reduced representations of molecules are often
applied. These so-called coarse-grained models are sufficient to
capture global collective motions on biologically relevant
spatial and temporal scales. However, due to reduction of the
degrees of freedom, coarse-grained models require
parameterizations of the potential energy function (force
field). Moreover, coarse-grained force field parameters are
typically not transferable between different molecules and
problems.
I will present our efforts to design an automatic
parameterization procedure to obtain force fields for reduced models of
biomolecules. The procedure for the optimization of potential
energy parameters is based on metaheuristic methods. I will also
show examples of applications to dynamics of proteins and nucleic
acids.
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