Description

Sidekick is a collection of scripts for performing high throughput, coarse grained molecular dynamics simulations of transmembrane helices, from intial sequences. Installed on Mac OS X clusters or workstations, this can be used to understand mutant effects or to predict high resolution behaviour.

Papers employing Sidekick

• A Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices
  Hall BA, Halim KA, Buyan A, Emmanouil B, Sansom MSP
  JCTC DOI
Primary and Secondary Dimer Interfaces of the FGFR3 Transmembrane Domain: Characterization via Multiscale Molecular Dynamics Simulations
Reddy T, Manrique S, Buyan A, Hall BA, Chetwynd A, Sansom MSP
Biochemistry 53 (2) DOI
Accommodation of a Central Arginine in a Transmembrane Peptide by Changing the Placement of Anchor Residues
Vostrikov VV, Hall BA, Sansom MSP, Koeppe RE
J Phys Chem B. 116 (43) DOI
Coarse-Grain Simulations Reveal Movement of the Synaptobrevin C-Terminus in Response to Piconewton Forces
Lindau M, Hall BA, Chetwynd A, Beckstein O, Sansom MSP
Biophysical Journal 103 (5) DOI
Multi-Scale Simulation of the Simian Immunodeficiency Virus Fusion Peptide
Crowet J, Parton DL, Hall BA, Steinhauer S, Brasseur R, Lins L, Sansom MSP
J Phys Chem B. 116(46) DOI
Exploring Peptide-Membrane Interactions with Coarse-Grained MD Simulations
Hall BA, Chetwynd AP, Sansom MSP
Biophysical Journal 100 (8) DOI
Transmembrane helix dynamics of bacterial chemoreceptors supports a piston model of signalling
Hall BA, Armitage JP, Sansom MSP
PLoS Computational Biology 7 (10) DOI
A helix heterodimer in a lipid bilayer: structure prediction of the structure of an integrin transmembrane domain via multiscale simulations
Kalli AC, Hall BA, Campbell ID, Sansom MSP
Structure 19 (10) DOI
Exploring peptide-membrane interactions with coarse-grained MD simulations
Hall BA, Chetwynd AP, Sansom MSP
Biophysical Journal 100 1940-1948 DOI
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations
Vostrikov VV, Hall BA, Greathouse DV, Koeppe RE, Sansom MSP
Journal of the American Chemical Society, 132(16), 5803-5811 DOI
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