All Stories

  1. Logic Programming for Organogenesis

    Article • Journal of The Royal Society Interface, June 2014, Royal Society Publishing

    Dr Benjamin A Hall

  2. Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices

    Article • Journal of Chemical Theory and Computation, April 2014, American Chemical Society (ACS)

    Dr Benjamin A Hall

  3. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

    Article • Journal of Chemical Theory and Computation, February 2014, American Chemical Society (ACS)

    Dr Benjamin A Hall

  4. Primary and Secondary Dimer Interfaces of the Fibroblast Growth Factor Receptor 3 Transmembrane Domain: Characterization via Multiscale Molecular Dynamics Simulations

    Article • Biochemistry, January 2014, American Chemical Society (ACS)

    Dr Benjamin A Hall

  5. Finding Instability in Biological Models

    Article • January 2014, Springer Science + Business Media

    Dr Benjamin A Hall

  6. Role of the C-terminal domain in the structure and function of tetrameric sodium channels

    Article • Nature Communications, September 2013, Springer Science + Business Media

    David Clapham, Dr Benjamin A Hall

  7. Multi-Scale Simulation of the Simian Immunodeficiency Virus Fusion Peptide

    Article • The Journal of Physical Chemistry B, November 2012, American Chemical Society (ACS)

    Dr Benjamin A Hall

  8. Accommodation of a Central Arginine in a Transmembrane Peptide by Changing the Placement of Anchor Residues

    Article • The Journal of Physical Chemistry B, October 2012, American Chemical Society (ACS)

    Dr Benjamin A Hall

  9. Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles

    Article • PLoS Computational Biology, September 2012, PLOS

    Dr Benjamin A Hall

  10. Coarse-Grain Simulations Reveal Movement of the Synaptobrevin C-Terminus in Response to Piconewton Forces

    Article • Biophysical Journal, September 2012, Elsevier

    Dr Benjamin A Hall

  11. How Lipid Headgroups Sense the Membrane Environment: An Application of 14N NMR

    Article • Biophysical Journal, September 2012, Elsevier

    Dr Benjamin A Hall

  12. Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity

    Article • Biochemistry, August 2012, American Chemical Society (ACS)

    Dr Benjamin A Hall

  13. Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors

    Article • Biology, July 2012, MDPI AG

    Dr Benjamin A Hall

  14. Coarse Grain Simulations Reveal Movement of Synaptobrevin C Terminus in Response to Piconewton Forces Suggesting a Novel Fusion Pore Mechanism

    Article • Biophysical Journal, January 2012, Elsevier

    Dr Benjamin A Hall

  15. Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling

    Article • PLoS Computational Biology, October 2011, PLOS

    Dr Benjamin A Hall

  16. A Helix Heterodimer in a Lipid Bilayer: Prediction of the Structure of an Integrin Transmembrane Domain via Multiscale Simulations

    Article • Structure, October 2011, Elsevier

    Dr Benjamin A Hall

  17. Exploring Peptide-Membrane Interactions with Coarse-Grained MD Simulations

    Article • Biophysical Journal, April 2011, Elsevier

    Dr Benjamin A Hall

  18. Molecular Dynamics Simulations of the Transmembrane Helix of the FGFR3 Receptor in POPC and DPPC

    Article • Biophysical Journal, February 2011, Elsevier

    Dr Benjamin A Hall

  19. Insertion Properties of Cftr Explored with High Throughput, Coarse Grain Molecular Dynamics

    Article • Biophysical Journal, February 2011, Elsevier

    Dr Benjamin A Hall

  20. How Transmembrane Model Peptides Affect Lipid Head Group Orientation: An Application of 14N NMR

    Article • Biophysical Journal, February 2011, Elsevier

    Dr Benjamin A Hall

  21. Bookshelf: a simple curation system for the storage of biomolecular simulation data

    Article • Database, December 2010, Oxford University Press (OUP)

    Dr Benjamin A Hall

  22. The Energetics of Transmembrane Helix Insertion into a Lipid Bilayer

    Article • Biophysical Journal, October 2010, Elsevier

    Dr Benjamin A Hall

  23. Changes in Transmembrane Helix Alignment by Arginine Residues Revealed by Solid-State NMR Experiments and Coarse-Grained MD Simulations

    Article • Journal of the American Chemical Society, April 2010, American Chemical Society (ACS)

    Dr Benjamin A Hall

  24. Sensitivity of Coarse Grain Models of Peptides to the Introduction of Charged Residues in Model Peptides and Bacterial Chemoreceptors

    Article • Biophysical Journal, January 2010, Elsevier

    Dr Benjamin A Hall

  25. Coarse-Grained MD Simulations and Protein−Protein Interactions: The Cohesin−Dockerin System

    Article • Journal of Chemical Theory and Computation, August 2009, American Chemical Society (ACS)

    Dr Benjamin A Hall

  26. High Throughput Coarse-Grained Simulations of the Insertion of Transmembrane Helices

    Article • Biophysical Journal, February 2009, Elsevier

    Dr Benjamin A Hall

  27. Characterization of Protein Conformational States by Normal-Mode Frequencies

    Article • Journal of the American Chemical Society, August 2007, American Chemical Society (ACS)

    Dr Benjamin A Hall

  28. Simulations of a Protein Translocation Pore:  SecY

    Article • Biochemistry, October 2006, American Chemical Society (ACS)

    Dr Benjamin A Hall

  29. Conformational Dynamics of M2 Helices in KirBac Channels:  Helix Flexibility in Relation to Gating via Molecular Dynamics Simulations

    Article • Biochemistry, October 2005, American Chemical Society (ACS)

    Dr Benjamin A Hall

  30. Conformational Dynamics of the Ligand-Binding Domain of Inward Rectifier K Channels as Revealed by Molecular Dynamics Simulations: Toward an Understanding of Kir Channel Gating

    Article • Biophysical Journal, May 2005, Elsevier

    Dr Benjamin A Hall

  31. Dynamite: a simple way to gain insight into protein motions

    Article • Acta Crystallographica Section D Biological Crystallography, November 2004, International Union of Crystallography

    Dr Benjamin A Hall