Volume 2 Supplement 1

3rd German Conference on Chemoinformatics: 21. CIC-Workshop

Open Access

Coarse-grained molecular models for high-throughput and multi-scale functional investigations

Chemistry Central Journal20082(Suppl 1):S14

https://doi.org/10.1186/1752-153X-2-S1-S14

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 [1] and potential points of interference by antibiotica, HIV protease [2] and its evolutionary dynamics en route to drug resistance [3]. 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 [6]. In addition we show recent results on further computational improvements and additional observations from a physicist's/chemist's point of view.

Authors’ Affiliations

(1)
Bioinformatics & Theo. Biology Group, Department of Biology, Technische Universität Darmstadt

References

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Copyright

© Hamacher 2008