Make_Exemplar Server Documentation



Overview

This generates an exemplar from a PDB structure as described here.

Tips

  1. Input PDB models should be processed to remove heteroatoms and non-standard residues (such as MSE).
  2. The choice of target residue(s) defines the location of the center of the local grid, as well as defining the contacting residues to filter out unrelated pockets. It is recommended to choose residues on opposing sides of the pocket that are centered on a cluster of residues with a high ddG in the protein complex (when exact binding pocket location is unknown) or centered over the known small molecule binding site.

Inputs

  1. PDB file: The pdb file of standard PDB format, processed to remove heteroatoms and non-standard residues (such as MSE).
  2. Target residues: Pockets are identified using a localized grid, keeping those touching both target residues. The grid is centered on the center of mass of the target residue(s) specified. One or two targets may be specified.
  3. Distance from solvent in to consider points "surface": (Advanced option) Lower values are useful when a small molecule binding pocket is very shallow.
  4. Grid Size:: (Advanced option) The local grid is built centered on the center of mass of the target residues. It extends Grid size units in each direction from the target residue(s). It often needs to be lowered when the surface distance (above) is lowered.

Please cite the following article when referring to results from our ROSIE server:

  1. Johnson DK and Karanicolas J. (2015),"Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions." Submitted.

  2. Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)". PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. Link



Please cite the following article when referring to results from our ROSIE server:

  1. Johnson DK and Karanicolas J. (2015),"Ultra-high-throughput structure-based virtual screening for small-molecule inhibitors of protein-protein interactions." Submitted.

  2. Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)". PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. Link

We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.


Make_Exemplar was developed by the Karanicolas lab at The University of Kansas