Coarse-grained molecular models for high-throughput and multi-scale functional investigations
© Hamacher 2008
Published: 26 March 2008
In this contribution we discuss the development, implementation, and the subsequent application of in silico, coarse-grained molecular models. The proposed approach allows for bridging a methodological gap between sequence-based bioinformatics and molecular dynamics simulations: molecular interactions can be modeled based on physio-chemical model in a highly parallelizable and high-throughput-ready fashion.
We demonstrate the broad applicability of such an approach by discussing the assembly of the bacterial ribosome  and potential points of interference by antibiotica, HIV protease  and its evolutionary dynamics en route to drug resistance . These methodologies were further applied to a signaling cascade in leukemia [4, 5] and can be used for design by e.g. global optimization techniques . In addition we show recent results on further computational improvements and additional observations from a physicist's/chemist's point of view.
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