SB2012

SB2012 Docking Database [2012.08.09 Initial Release]

The downloads presented here refer to the publication "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments". The base version of the database is presented as Receptors, Ligands and Spheres, which is applicable to any docking program. The spheres and grids are meant to be used with any version of the DOCK program. SB2010 is an on-going project; more structures and related resources will be added in the future. Work on SB2011 testset release is in progress.

Resource	Filename
Receptors, Ligands and Spheres	SB2012.08.09_rec.lig.sph.tar.gz
Energy and Bump Grids	2012.08.09_grids.tar.gz

Note: The DOCK energy and bump grids provided are binary files (13GB download). These were generated on an Intel Xeon, and should work fine with DOCK 4 or greater. Some platforms (e.g. ibm aix) use a different endian ordering and would require the grids to be regenerated. The grids are provided for convenience, and can be generated independently from the receptor files. The receptor and ligand mol2 files should also be compatible with most other commercial and academic docking programs. If you would like to suggest alternative file formats (pdb,sdf etc) to facilitate use with a particular tool, please contact the authors.

DOCK Input Files

These are the DOCK input files used to evaluate the database.

Resource	Filename
Rigid (RGD)	RGD
Fixed Anchor (FAD)	FAD
Flexible Ligand (FLX)	FLX

Copyright

This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useable by the docking community, both academic and commercial institutions. The manuscript for this work has been accepted and is currently in press.

Contact Information

Please contact if you face any problems.
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.