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Computational and theoretical biophysics

This section incorporates all aspects of computational and theoretical biophysics including: theory, modeling, simulation and nanotechnology.

  1. Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied ext...

    Authors: Asli Yildirim, Nathalie Brenner, Robert Sutherland and Michael Feig

    Citation: BMC Biophysics 2018 11:8

    Content type: Research article

    Published on:

  2. The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational sc...

    Authors: Aarón Ayllón Benítez, José Ginés Hernández Cifre, Francisco Guillermo Díaz Baños and José García de la Torre

    Citation: BMC Biophysics 2015 8:11

    Content type: Research Article

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  3. Cells continuously undergo DNA damage from exogenous agents like irradiation or genotoxic chemicals or from endogenous radicals produced by normal cellular metabolic activities. DNA strand breaks are one of th...

    Authors: Michael Junk, Judy Salzwedel, Thilo Sindlinger, Alexander Brkle and Maria Moreno-Villanueva

    Citation: BMC Biophysics 2014 7:9

    Content type: Methodology article

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  4. The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-P...

    Authors: Phanourios Tamamis, Chris A Kieslich, Gregory V Nikiforovich, Trent M Woodruff, Dimitrios Morikis and Georgios Archontis

    Citation: BMC Biophysics 2014 7:5

    Content type: Research article

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  5. Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to con...

    Authors: Paolo Mereghetti, Michael Martinez and Rebecca C Wade

    Citation: BMC Biophysics 2014 7:4

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Biophysics 2020 12:2

  6. Keratins are important structural proteins found in skin, hair and nails. Keratin Intermediate Filaments are major components of corneocytes, nonviable horny cells of the Stratum Corneum, the outermost layer o...

    Authors: Anna Akinshina, Etienne Jambon-Puillet, Patrick B Warren and Massimo G Noro

    Citation: BMC Biophysics 2013 6:12

    Content type: Research article

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  7. Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces b...

    Authors: Bogdan I Costescu and Frauke Gräter

    Citation: BMC Biophysics 2013 6:5

    Content type: Methodology article

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  8. The V3 loop of the glycoprotein gp120 of HIV-1 plays an important role in viral entry into cells by utilizing as coreceptor CCR5 or CXCR4, and is implicated in the phenotypic tropisms of HIV viruses. It has be...

    Authors: Aliana López de Victoria, Chris A Kieslich, Apostolos K Rizos, Elias Krambovitis and Dimitrios Morikis

    Citation: BMC Biophysics 2012 5:3

    Content type: Research article

    Published on: