Difference between revisions of "Rizzo Lab Downloads"
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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. | 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 (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. | |
| − | $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. | $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. | ||
Revision as of 15:48, 9 August 2010
Contents
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.
| 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 |
|---|---|
| HIV RT | 21 |
| 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 |
| COX | 7 |
| 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 docking results with the top scored pose for each pdb code. These results were produced with DOCK 6.4, using the dock input files shown above. Please note that you will get slightly different results, depending on the environment you use to compile the dock binaries.
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 (in absence of the receptor) 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.
Copyright
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 
if you face any problems.
