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cachemoi edited this page Oct 25, 2015 · 16 revisions

Welcome to the mol-vis-hack wiki! See the sidebar links to view more information.

A major challenge in modern biology lies in understanding how proteins interact with each other. By visualising and annotating 3 dimensional structures researchers are able to identify key binding sites for relevant ligands. Amongst other things this can lead to the identification of drug targets.

An example of this is leucine zippers. This protein motif is very common and is found in numerous transcription factors. Leucine zippers are proteins dimers; they are composed of two separable modules. Like many protein structures, they were discovered by biochemists who simply looked at their modelled structures and recognised binding sites.

Solving protein structures and finding binding sites using computers is still in its infancy and highly inaccurate. We need a deeper understanding of much of the physics behind it before we can rely on it. This means that the most effective way to identify binding sites and solve structures is still to get humans (preferably trained biochemists) to look at 3D models of the proteins. This was made obvious when some researchers created a game in which people were asked to fold a chain of amino acids to get a good score. They were able to predict protein structure much more accurately than the best available computer software.

This is where our hack comes in. Using the browser 3D viewer provided by Autodesk we are able to provide a beautiful, modular, and user annotated 3D model of the proteins. The atom location data can be found on the rapidly expanding Protein data base (PDB). Today most online protein 3D viewers are rather crude and do not allow user to annotate different parts of the protein. This

  1. PDB code --> VRML 2, .wrl file (via UCSF Chimera) --> .fbx file (via Blender)
  2. Hosting models in LMV via their bucket storage
  3. Checking against a list of already processed PDB codes, or generation of new 3D models and uploading to Autodesk.com
  4. Potential room for development: working with extensions given a structure
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