Tutorial
This tutorial walks you to the process of finding hits for the thrombin-trypsin inhibitor complex.
Searching for the keywords “thrombin” and “inhibitor” provides a list of hits. For the selected entry 1BTH various types of information are shown, as well as a listing of the clusters the complex belongs to. General properties of the PDB entry are accompanied by 3D views of the full complex and detailed views of the peptide binding site generated by Yasara. The binding energy between protein and peptide as calculated by the FoldX force field is shown together with details for the hydrogen bond interactions. Various statistics regarding the secondary structure content and flexibility parameters for the binding site are listed, as well as direct links to relevant databases. The peptides are annotated with naturally occurring backbone variations using fragment clusters from the BriX database.
