Jocelyn Sunseri edited section_Compound_Libraries_Unique_to__.tex  about 8 years ago

Commit id: e1fd7b2f831bd7a6f50bc6d54551384b44d8fbee

deletions | additions      

       

\subsection{Library Creation}  Users may submit their own libraries for screening. In the spirit of the open access and open-source nature of Pharmit, users are encouraged to make their submitted libraries publicly accessible, in which case they are available to all users for screening as a user contributed library. However, registered users have the ability to  create a private library, as well as remove or update previously submitted libraries. In order to create a library, compounds may be provided in 2D SMILES format, in which case RDKit (\url{rdkit.org}) and the UFF force field \cite{Rappe_1992} are used to generate up to 10 3D conformers for each compound. This approach has been shown to generate high quality conformations \cite{Ebejer_2012}. Alternatively, the user may provide compounds in the 3D SDF format, in which case the provided structures are assumed to be valid conformers and are used directly.