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Coarse-grained molecular models for high-throughput and multi-scale functional investigations
Chemistry Central Journal volume 2, Article number: S14 (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.
Hamacher K, Trylska J, McCammon JA: Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput Biol. 2006, 2: e10-10.1371/journal.pcbi.0020010.
Hamacher K, McCammon JA: Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. J Chem Theo Comp. 2006, 2: 873-10.1021/ct050247s.
Hamacher K: Gene. 2007, submitted
Hamacher K, Hübsch A, McCammon JA: A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys. 2006, 124: 164907-164914. 10.1063/1.2185645.
Hamacher K: Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design. J Comp Chem. 2007, 28: 2576-2580. 10.1002/jcc.20759.
Hamacher K: Adaptation in Stochastic Tunneling Global Optimization of Complex Potential Energy Landscapes. Europhys Lett. 2006, 74: 944-950. 10.1209/epl/i2006-10058-0.
Hamacher K: Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis. Physica A. 2007, 378: 307-314. 10.1016/j.physa.2006.11.071.
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Hamacher, K. Coarse-grained molecular models for high-throughput and multi-scale functional investigations. Chemistry Central Journal 2, S14 (2008) doi:10.1186/1752-153X-2-S1-S14
- Molecular Dynamic
- Molecular Dynamic Simulation
- Dynamic Simulation
- Global Optimization