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\section{Query Definition}  Table of Contents:  Getting Started  Initiating a Search  Visualization  Pharmacophore Representations  Shape Constraints  Hit Reduction and Feasibility Screening  Database Selection  Saving and Loading Sessions  Managing Search Results  Saving and Minimizing Results  User-submitted Databases  Related Software  Additional Help  Getting Started  pharmit is a web server that facilitates virtual screening: it enables users to search for small molecules based on their structural and chemical similarity to another small molecule, with the goal of identifying those that bind to a target molecule (typically a protein receptor or enzyme). The search can take as input either a small molecule, a set of pharmacophore features (which will be subsequently described in greater detail), or both a protein and a small molecule for which a putative binding pose is known. These may be obtained from the Protein Data Bank (PDB) or uploaded by the user directly, using one of the two options provided on the main page.  Getting started  Initiating a Search