deletions | additions       diff --git a/section_Energy_Minimization_The_query__.tex b/section_Energy_Minimization_The_query__.tex  index 4923802..226482c 100644  --- a/section_Energy_Minimization_The_query__.tex  +++ b/section_Energy_Minimization_The_query__.tex 
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\section{Energy Minimization}  The query-aligned poses returned by pharmacophore and shape search are fully determined by the query. They are not influenced by interactions with the receptor. Furthermore, although the pose of the result is optimized to match the query, the conformation of the result is taken directly from the search database. Energy minimization of results optimizes both the pose and conformation of identified hits with respect to the provided receptor using the AutoDock Vina \cite{Trott_2009} scoring function and smina \cite{smina}, a fork of AutoDock Vina with enhanced minimization functionality.  \cite{smina}  Pressing the "Minimize" button before saving allows the user to assess the favorability of the interaction between the protein and the ligands returned by the search. This feature energy minimizes the results using smina, Minimized compounds adopt  a fork of AutoDock Vina, using the default Vina scoring function. Using this scoring function, conformation at  a more negative score indicates that the corresponding interaction is more favorable local minimum and are sorted  according to the scoring function's model of protein-ligand interaction; thus large positive scores indicate unfavorable interactions, and large predicted binding affinity in kcal/mol (more  negative scores indicate values are  more favorable interactions. If the user chooses to minimize the results, they may be sorted by score or favorable). Also reported is a minimized  RMSD of (mRMSD) that is  the minimized pose from RMSD between  the starting query-aligned  pose(which was aligned to the query) by pressing the name of the sorting method. Additional filters may also be applied by setting values for maximum score, maximum minimized RMSD,  andrequesting that only one pose be retained for each conformer. Once the filters have been set as desired, the user should press "Apply" to enforce them. Pressing "Save" after minimizing the results generates a single sdf file containing  the minimized structures that includes their minimized scores; it is often useful to rank the structures in order pose. This provides an indication  of increasing score so that how far  the best results can be reviewed first. We additionally recommend that compound has deviated from the original query. Minimized  results may  be sorted and  filtered by affinity and  mRMSD(e.g. 2Å)  to eliminate poses with unfavorable binding energies (e.g., $>-6$ kcal/mol) and  significant deviations from the original query. query (e.g. $2\AA$). The results can be saved, complete with scoring annotations, as a compressed SDF structure file.