deletions | additions       diff --git a/section_Example_To_demonstrate_Pharmit__.tex b/section_Example_To_demonstrate_Pharmit__.tex  index 7e747d0..ba386f6 100644  --- a/section_Example_To_demonstrate_Pharmit__.tex  +++ b/section_Example_To_demonstrate_Pharmit__.tex 
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Beginning on the Pharmit main page, the user initiates a search by typing `2SRC' into the `start from PDB' box. This will retrieve the ligand names, ANP and PTR, from the PDB file, and they are displayed in the dropdown menu next to the PDB code box. The user then selects the ANP ligand and, for this example, chooses to ignore the binding site waters. After clicking `submit,' the user will be taken to the main Pharmit interface. A set of interacting pharmacophore features will be automatically generated from the protein-ligand complex.    Pharmit identifies 26 pharmacophore features in ANP, 14 of which are interacting with the receptor. Searching with this default query yields no hits as it is overly specific. In general, we find that queries rarely benefit from having more than 5 distinct features.  To generate a useful query for 2SRC, we rationally target the canonical hinge site, with which ANP strongly interacts, by including a hydrogen donor and acceptor and two aromatics. aromatics to mimic the adenine moiety.  We anchor the query at the other side of the pocket by including a hydrogen acceptor, for a total of five features. While this query is reasonable given the structure of the kinase, strong interactions with functional groups in the pocket are possible outside of the narrow constraints derived from the small donor/acceptor tolerance spheres; as it is, few hits are returned. Thus the tolerance spheres for donors and acceptors are increased to 1.0. Finally, several features included in the query are likely interacting with a single group in the pocket, making it reasonable to impose a directionality on these features. The hydrogen acceptor interacting at the hinge site is given a $\phi$ of 90 and $\psi$ of 45, and the second aromatic is given a $\phi$ of 10 and $\psi$ of -50. The DUDe 2SRC benchmark set, which consists of small molecules known to bind 2SRC as well as structurally similar compounds that do not bind, is a contributed library available to search within Pharmit, and this is used to validate the pharmacophore. Searching generates 39 hits, with an enrichment factor of 41.1.