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This article is part of the supplement: 3rd German Conference on Chemoinformatics: 21. CIC-Workshop

Open Access Oral presentation

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

Kay Hamacher

Author Affiliations

Bioinformatics & Theo. Biology Group, Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany

Chemistry Central Journal 2008, 2(Suppl 1):S14 doi:10.1186/1752-153X-2-S1-S14


The electronic version of this article is the complete one and can be found online at: http://www.journal.chemistrycentral.com/content/2/S1/S14


Published:26 March 2008

© 2008 Hamacher

Oral presentation

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.

References

  1. Hamacher K, Trylska J, McCammon JA: Dependency Map of Proteins in the Small Ribosomal Subunit.

    PLoS Comput Biol 2006, 2:e10. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  2. Hamacher K, McCammon JA: Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems.

    J Chem Theo Comp 2006, 2:873. Publisher Full Text OpenURL

  3. Hamacher K:

    Gene. 2007.

    submitted

    OpenURL

  4. Hamacher K, Hübsch A, McCammon JA: A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.

    J Chem Phys 2006, 124:164907-164914. PubMed Abstract | Publisher Full Text OpenURL

  5. Hamacher K: Information Theoretical Measures to Analyze Trajectories in Rational Molecular Design.

    J Comp Chem 2007, 28:2576-2580. Publisher Full Text OpenURL

  6. Hamacher K: Adaptation in Stochastic Tunneling Global Optimization of Complex Potential Energy Landscapes.

    Europhys Lett 2006, 74:944-950. Publisher Full Text OpenURL

  7. Hamacher K: Energy landscape paving as a perfect optimization approach under detrended fluctuation analysis.

    Physica A 2007, 378:307-314. Publisher Full Text OpenURL