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Mechanosensation
and ion channels | Software
we use
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Dr.
H. Robert Guy group
The group develops structural models for the transmembrane portions of
membrane proteins, with special emphasis on proteins that form ion channels |
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Dr.
Ching Kung lab
The laboratory studies sensory transduction in microbes with special
emphasis on ion channels |
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Dr.
Paul Blount lab
The laboratory studies mechanosensitive channels, primarily from microbes.
They are interested in the molecular mechanisms of gating of these channels,
the role they play in microbial physiology, and the possibility of utilizing
these channels as sensors in small mechanical devices |
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Dr.
Boris Martinac lab
Mechanosensory transduction (biophysics, molecular biology and pharmacology
of prokaryotic - bacterial and archaeal - mechanosensitive (MS) ion
channels). Biophysics and molecular biology of bacterial porins. |
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Dr.
Ian Booth lab
One of lab's major research activities is the analysis of the structure and function of bacterial ion channels and efflux
systems - mechanosensitive (MscL, MscS, MscM, KefA), ligand-gated (KefB, KefC), Shaker-like (Kch) and chloride (CLC). |
| Dr.
Eduardo Perozo lab
Structural and Functional Studies of Potassium and Mechanosensitive Ion Channels and Membrane Proteins |
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Dr. Klaus Schulten group
Theoretical and Computational Biophysics Group - development of molecular
dynamics and visualization software and broad spectrum of simulational and
theoretical research areas, including mechanosensitive channels.
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Dr.
Fred Sachs lab
The Sachslab is interested in all forms of mechanosensitivity and .
They are using Electrophysiological techniques, atomic force microscopy (AFM),
calcium imaging, fluorimetry and membrane mechanics to investigate all
aspects of mechanotransduction |
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Dr.
Douglas C. Rees group
Research in the Rees group emphasizes the general area of structural
bioenergetics, which seeks to describe the molecular basis of energy
transduction and mechanosensation processes
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Dr.
Dennis A. Dougherty lab
The group conducts research in organic and bioorganic chemistry. The
major focus of the group seeks a chemical-scale understanding of ion
channels and neuroreceptors.
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| Clampex 9
- Electrophysiological data acquisition and review
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| Clampfit
9 - Electrophysiological data analysis; channel dwelling time
calculations, exponential fits of inactivation
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| QuB - Software for Single Channel Analysis,
developed in laboratory of Frederick Sachs in collaboration with Anthony Auerbach;
channel dwelling time calculations, 'on' and 'off' rate constants
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| Matlab - A high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation.
We have developed a couple of software packages in Matlab, which we use
routinely in our lab (address questions and comments to Andriy
Anishkin):
HISTAN - A program package for histogram-based analysis of patch-clamp
recordings
PDBAN - A package for handling and analysis of PDB structures
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| GetArea
- Web-based Program for Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies, and Their Gradients for Macromolecules;
developed in Werner Braun lab.
We prepared an expanded GETAREA library of atom types for proteins,
compatible with wider range of PDB structures.
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| NAMD
- A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems,
developed in Klaus Schulten Lab; steered molecular dynamics, embedded Tcl/Tk
scripting language.
We have developed a set of scripts (A. Anishkin) allowing to
perform steered simulations with time-varying restrains and complex
applied forces.
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| VMD
- A molecular visualization program for displaying, animating, and analyzing large biomolecular systems,
developed in Klaus Schulten Lab; embedded Tcl/Tk scripting language.
Check out our custom VMD startup
file and scripts
(A. Anishkin) for analysis and visualization of molecular structure and
simulation results.
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| Crimson Editor
- A freeware professional source code editor for Windows (by Ingyu Kang);
custom syntax highlighting. We have custom syntax files (A.
Anishkin) prepared for VMD, NAMD.
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| Total commander
- A powerful file manager for Windows (by Christian Ghisler); built in
FTP client, versatile file rename system, various plug-in
extensions.
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| IrfanView -
one of the most popular freeware viewers and editors worldwide (by Irfan
Skiljan); batch image processing.
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| VNC - A
cross-platform remote control software.
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