Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach

A. Bujotzek, M. Weber – 2009

The understanding of biological ligand–receptor binding processes is relevant for a variety of research topics and assists the rational design of novel drug molecules. Computer simulation can help to advance this understanding, but, due to the high dimensionality of according systems, suffers from the severe computational cost. Based on the framework provided by conformation dynamics and transition state theory, a novel heuristic approach of simulating ligand–receptor binding processes is introduced, which is not dependent on calculating lengthy molecular dynamics trajectories. First, the relevant portion of conformational space is partitioned with meshless methods. Then, each region is sampled separately, using hybrid Monte Carlo. Finally, the dynamical binding process is reconstructed from the static overlaps between the partial densities obtained in the sampling step. The method characterizes the metastable steps of the binding process and can yield the corresponding transition probabilities.

Titel
Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach
Verfasser
A. Bujotzek, M. Weber
Datum
2009
Kennung
10.1142/s0219720009004369
Zitierweise
J. Bioinform. Comput. Biol., 2009, 7 (5), 811-831
Art
Text
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