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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 [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.
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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.
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Hamacher K: Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design. J Comp Chem. 2007, 28: 2576-2580. 10.1002/jcc.20759.
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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.
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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
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Keywords
- Leukemia
- Molecular Dynamic
- Molecular Dynamic Simulation
- Dynamic Simulation
- Global Optimization
