BEST1 variants are responsible for Best disease and for some cases of the adult-onset form of vitelliform macular dystrophy. Variants (also known as mutations) in the BEST1 and PRPH2 genes cause vitelliform macular dystrophy. The two forms of vitelliform macular dystrophy each have characteristic changes in the macula that can be detected during an eye examination. The adult-onset form begins later, usually in mid-adulthood, and tends to cause vision loss that worsens slowly over time. The early-onset form (known as Best disease) usually appears in childhood the age at which symptoms begin and the severity of vision loss vary widely. Researchers have described two forms of vitelliform macular dystrophy with similar features. Vitelliform macular dystrophy typically does not affect side (peripheral) vision or the ability to see at night. As a result, people with this disorder often lose their central vision, and their eyesight may become blurry or distorted. Over time, large amounts of this substance can damage cells that are critical for clear central vision. Vitelliform macular dystrophy causes a fatty yellow pigment (called lipofuscin) to build up in cells underlying the macula. The macula is responsible for sharp central vision, which is needed for detailed tasks such as reading, driving, and recognizing faces. Specifically, vitelliform macular dystrophy disrupts cells in a small area near the center of the retina called the macula. This disorder affects the retina, the specialized light-sensitive tissue that lines the back of the eye.
VMD CITATION LICENSE
To use MEMBPLUGIN you need to comply with the terms of the GNU General Public License 3.0 (see the accompanying COPYING file).Vitelliform macular dystrophy is a genetic eye disorder that can cause worsening (progressive) vision loss. MEMBPLUGIN: studying membrane complexity in VMD.
VMD CITATION SOFTWARE
The plugin is described in the Bioinformatics paper MEMBPLUGIN: studying membrane complexity in VMD, which you should cite if you use this software in publications. Run the following commands for usage info: If you are in text-only mode, you might need to load mempluguin package first with 'package require membplugin'. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation. Command-line interfaceĪll of the tools' functions can be accessed from VMD's scripting environment. The documents are distributed together with the simulation data necessary to fully reproduce the analysis. an advanced case study, showing the analysis performed on cholesterol-enriched membranes.a step-by-step tutorial, suitable for beginners or first-time users and.Two extended write-ups show the use of MEMBPLUGIN on realistic systems: The Lipid Tilt Tool computes tilt angles with respect to the bilayer's normal.Īdditionally, links are provided for the external Diffusion Coefficient and Density Profile tools.The Area per Lipid Tool tool computes the average area per lipid of the membrane simulation along with the specific area per lipid of each lipid species.The Interdigitation Tool measures the amount of interdigitation present between the two leaflets.The Membrane Thickness Tool computes bilayer overall thickness and its 2-D thickness map.The SCD Order Parameter Tool computes the Scd (deuterium order parameters) of lipid tails.See the linked wiki pages for more information. The following tools are currently included in MEMBPLUGIN. Additionally, the membplugin_lipids macro is available to indicate the residue names listed in the configuration, notably those supported by the CHARMM-GUI membrane builder. Where atom selections are required, VMD's atom selection syntax applies. See details in the requirements list page. The systems to be analyzed have to satisfy certain constraints, notably they have to be oriented so that the bilayer normal is along the Z axis, and molecules need not be broken at the periodic cell boundaries. to align it, make sure you save it on disk. If you modify your current molecule, e.g. Note that all analysis is performed on-disk, not on the currently loaded molecule. General usageĪfter installation, the plugin's Main Window is accessible from VMD's Extensions>Analysis>Membrane Analysis Tool (MEMBPLUGIN). Please see the Installation page and/or the INSTALL.txt file. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. MEMBPLUGIN Studying membrane complexity in VMD
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