Rizzo Lab Downloads

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SB2010 Docking Database [2010.05.19 Initial Release]

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. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.

Resource Filename
Receptors, Ligands and Spheres SB2010.05.19_rec.lig.sph.tar.gz
Energy and Bump Grids To be released
Alternate Ligand Charge Models To be released
Best Flex Docked Poses To be released
DOCK Sample Inputs RGD FAD FLX
Flexibility Subset Lists 7orless 8to15 15+ all

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

SB2010 Ligand Flexibility Subsets

The Flexibility Subset Lists divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges.

Resource Filename
7 or less 7orless
8 to 15 8to15
15+ 15+
All Systems all

SB2010 Protein Families [2010.05.19 Initial Release]

The 25 large protein families in the database are presented as subsets below. Another 25 smaller families (i.e less than 7 members) are also present in the database.

Protein Family Size
Factor Xa 41
Neuraminidase 43
Sialidase 11
Ribonuclease T1 7
OMP Decarboxylase 7
Estrogen Receptor 45
T4 Lysozyme 13
Beta Trypsin 29
Streptavidin 8
Thrombin 37
Tyrosine Phosphatase 20
HMG COA Reductase 20
Ribonuclease A 14
Alpha Trypsin 46
Acetylcholinesterase 19
HIV Protease 60
Thermolysin 26
Carboxypeptidase A 8
Matrix Metalloprotease 14
Egg Lysozyme 14
Phospholipase A2 15
Thymidylate Synthase 12
Carbonic Anhydrase 29

Sample Docking Results

Sample flexible ligand results with the top scored pose for each pdb code. These results were produced with DOCK 6.4, using the flex docking input file shown above.

Sample Flex Results

Unbiased Ligands

In the regular testset distribution, the ligand provided is the native crystal structure pose. In order to test if starting with the correct conformation initially biased the results of flexible docking experiments, we also provide 'unbiased' ligands.

$system.lig.am1bcc.unbiased_gasmin.mol2 is minimized in gas phase with the MMFF94x forcefield with the MOE 2009.10 program. $system.lig.am1bcc.unbiased_gasmin.trans.mol2 is the same minimized molecule, rigid-body translated and rotated (transformed) from the starting coordinates by about 15A.

Unbiased Ligands


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

Contact Information

Please contact Sudipto.email.png if you face any problems.