Permalink
Switch branches/tags
Nothing to show
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
56 lines (36 sloc) 1.91 KB

Sites

Ligand interactions

This video demonstrates how to visualize receptor-ligand interactions in a PDB file by providing a PDB code, or by uploading your own file.

  • The interactions are listed in table format, and it is possible to filter and order interactions by the values in each column.
  • An interactive 3D viewer showing only the ligand and interacting residues from the receptor is available.
  • Snake and Helix box plots highlighting the interacting residues in red can be downloaded.
Your browser does not support the video tag.

Question

  • Look up the recptor ligand interactions in PDB structure 3RZE? How many interactions are found?

Site search - from PDB complex

This video demonstrates how to create a binding site definition by providing a PDB code, or by uploading your own file. The resulting site definition can be used to search for receptors with a similar binding site.

  • A binding site definition can be extracted from a provided PDB code, or an uploaded PDB file.
  • First select the set of receptors that should be compared the the site definition.
  • Once the PDB file has been processed, the site definition can be reviewed and modified.
  • Note the "Min. match" field, which determines how many interactions must match for a receptor to be considered a match.
  • The results page shows a list of matching receptors, followed by a list of non-matching receptors.
Your browser does not support the video tag.

Question

  • Create a site definition using PDB structure 3RZE? How many interactions are found?