deletions | additions       diff --git a/section_Example_To_demonstrate_Pharmit__.tex b/section_Example_To_demonstrate_Pharmit__.tex  index dd1553a..e14757d 100644  --- a/section_Example_To_demonstrate_Pharmit__.tex  +++ b/section_Example_To_demonstrate_Pharmit__.tex 
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\section{Example}  To demonstrate Pharmit's capabilities, this section describes a virtual screen of Tyrosin-protein kinase C-SRC in based off a  complexwith AMP-PNP  (PDB 2SRC). 2SRC) with a nonhydrolyzable ATP analog (ANP).  The resulting query is available as an interactive example from the Pharmit examples page. For this example we submitted the compounds of the the DUDe  Beginning on the Pharmit main page, the user initiates a search by typing `2SRC' into the `start from PDB' box. This will retrieve the ligands, AMP ANP  and PNP, PTR,  in 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 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  which the user should select a subset to represent a pharmacophore. Choosing more than five features will generally yield few or no results if tolerance spheres are of size 1.0 or smaller, since this produces a very specific query for which there are likely no hits in the database. To generate a useful query to find hits for 2SRC, we target the canonical hinge site, with which ANP strongly interacts, by including a hydrogen donor and acceptor, as well as two aromatics. 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.