Difference between revisions of "SB2010"
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! style="width:25%" !|Clash List | ! style="width:25%" !|Clash List | ||
|- | |- | ||
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/CARBONIC_ANHYDRASE_rec.lig.tar.gz Carbonic Anhydrase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/CARBONIC_ANHYDRASE.tar.gz Carbonic Anhydrase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYbw.png Matrix] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
|- | |- | ||
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/HIV_PROTEASE_rec.lig.tar.gz HIV Protease] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/HIV_PROTEASE.tar.gz HIV Protease] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYbw.png Matrix] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
|- | |- | ||
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/NEURAMINIDASE_rec.lig.tar.gz Neuraminidase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/NEURAMINIDASE.tar.gz Neuraminidase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYbw.png Matrix] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
|- | |- | ||
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/REVERSE_TRANSCRIPTASE_rec.lig.tar.gz Reverse Transcriptase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/REVERSE_TRANSCRIPTASE.tar.gz Reverse Transcriptase] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYbw.png Matrix] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
|- | |- | ||
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/THERMOLYSIN_rec.lig.tar.gz Thermolysin] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/THERMOLYSIN.tar.gz Thermolysin] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYbw.png Matrix] |
| − | || [ | + | || [https://george.ams.stonybrook.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
|} | |} | ||
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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. | 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. | ||
| − | [ | + | [https://george.ams.stonybrook.edu/SB2010/2010.08.09_top_scored_poses.tar.gz Sample Docked Poses] |
== Alternative Ligand Starting Geometries == | == Alternative Ligand Starting Geometries == | ||
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XXXX.lig.mmff94x_gasmin.mol2 are alternative initial ligand coordinates obtained from gas-phase minimization (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. MMFF94x charges are assigned to the ligands before minimization. | XXXX.lig.mmff94x_gasmin.mol2 are alternative initial ligand coordinates obtained from gas-phase minimization (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. MMFF94x charges are assigned to the ligands before minimization. | ||
| − | [ | + | [https://george.ams.stonybrook.edu/SB2010/2010.09.10_mmff94x_ligs.tar.gz MMFF94x Ligands] |
Starting geometries optimized with gaff, opls, am1 and pm3mm were generated as well. These are available on request. | Starting geometries optimized with gaff, opls, am1 and pm3mm were generated as well. These are available on request. | ||
Latest revision as of 13:57, 30 August 2023
For more Rizzo Lab downloads: Rizzo Lab Downloads
Contents
SB2010 Docking Database [2010.05.19 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.
| Resource | Filename |
|---|---|
| Receptors, Ligands and Spheres | SB2010.05.19_rec.lig.sph.tar.gz |
| Energy and Bump Grids | 2010.09.13_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 |
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 |
Aligned Families
Alignment for 5 protein families are presented. Each receptor was aligned to the first PDB code in the corresponding family list above. The same transformation was then applied to the ligand. The Aligned Family column has only the aligned receptor and ligand files. Pre-computed DOCK energy and bump grids (300MB-1.4GB for each set) are also available for the aligned families in the "Family+Grids" column.
| Aligned Family | Family+Grids | Clash Matrix | Clash List |
|---|---|---|---|
| Carbonic Anhydrase | Carbonic Anhydrase | Matrix | Clash List |
| HIV Protease | HIV Protease | Matrix | Clash List |
| Neuraminidase | Neuraminidase | Matrix | Clash List |
| Reverse Transcriptase | Reverse Transcriptase | Matrix | Clash List |
| Thermolysin | Thermolysin | Matrix | Clash List |
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.
Alternative Ligand Starting Geometries
XXXX.lig.mmff94x_gasmin.mol2 are alternative initial ligand coordinates obtained from gas-phase minimization (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. MMFF94x charges are assigned to the ligands before minimization.
Starting geometries optimized with gaff, opls, am1 and pm3mm were generated as well. These are available on request.
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 is "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments".
Contact Information
Please contact a current member of the lab if you face any problems. Contact information can be found here.
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.
