E-Novo Protocol Updated in DS255/PP752
(J. Chem. Inf. Model., 2009, 49 (7), pp 1797–1809)

This protocol prepares protein-ligand complexes from a receptor, a set of query compounds and an 3D scaffold within active site, performs core-constrained docking using CDocker, and scores top ranking poses based on cdocker interaction energy or/and binding energy with implict solvation models. Pipeline Pilot [v752] Chemistry and Discovery Studio [v255] CHARMm component collections are required.

The input files include:
• Program_Cmpds_Source (*.sdf)// SD file that contains larger set of program structures and corporate ID e.g. MOL_ID, may contain biological screening data typically pEC50, pIC50 or pKi
• Receptor_Source (*.mol2)// MOL2 file containing the prepared protein information
• Fixed_Scaffold_Source (*.sd or *.mol)// MOL RG file with labeled R groups (To prepare scaffold in DS, remove all Hydrogen atoms except for those considered as R groups, save it in sd or mol, then replace Hi with Ri in a text editor...)
• Fixed Core// User specified core atoms to be fixed, e.g. 1:16 [fix heavy atoms 1-16]
• Run_Directory// Location of run directory containing all input, output and run time data files

Please note that it is not officially supported by Accelrys R&D. This updated version has not been fully validated by either BMS or Accelrys. The user might not be able to reproduce the result from DS1.7 because of the change in CHARMm version and the modifications on CDocker and GBSA implicit solvent model