deletions | additions       diff --git a/section_Example_To_demonstrate_Pharmit__.tex b/section_Example_To_demonstrate_Pharmit__.tex  index 6f140b6..daa42e0 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 presents a timeline of virtual screening for Tyrosin-protein kinase C-SRC, C-SRC  in complex with AMP-PNP; this AMP-PNP. This compound  is PDB code 2SRC, and the reader can reproduce the results of this section by visiting the Pharmit examples page and clicking on the 2SRC link, or by following the process described in this section. Beginning on the Pharmit main page, the user should initiate a search by typing '2SRC' into the 'start from PDB' box. This will retrieve the ligands in the PDB file, which are displayed in the dropdown menu next to the PDB code box; the user may select any ligand in the PDB file to generate a pharmacophore. If it is not currently selected, the user should choose ANP and ignore the binding site waters, then click 'submit.' The user will then be taken to the graphical workspace where queries are generated, and a set of interacting features will be automatically generated from 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.