Difference between revisions of "Rizzo Lab Downloads"
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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. Since energy and bump grids for the aligned receptors are also included, these files are fairly large (300MB-1.4GB). | 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. Since energy and bump grids for the aligned receptors are also included, these files are fairly large (300MB-1.4GB). | ||
| − | [http://george.ams.sunysb.edu/SB2010/CARBONIC_ANHYDRASE.tar.gz Carbonic Anhydrase] [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYbw.png Matrix] [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | + | {| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%" |
| − | + | |- style="background:lightblue" | |
| − | [http://george.ams.sunysb.edu/SB2010/HIV_PROTEASE.tar.gz HIV Protease] [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYbw.png Matrix] [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | + | ! style="width:50%" !|Aligned Family |
| − | + | ! style="width:25%" !|Clash Matrix | |
| − | [http://george.ams.sunysb.edu/SB2010/NEURAMINIDASE.tar.gz Neuraminidase] [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYbw.png Matrix] [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | + | ! style="width:25%" !|Clash List |
| − | + | |- | |
| − | [http://george.ams.sunysb.edu/SB2010/REVERSE_TRANSCRIPTASE.tar.gz Reverse Transcriptase] [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYbw.png Matrix] [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | + | || [http://george.ams.sunysb.edu/SB2010/CARBONIC_ANHYDRASE.tar.gz Carbonic Anhydrase] |
| − | + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYbw.png Matrix] | |
| − | [http://george.ams.sunysb.edu/SB2010/THERMOLYSIN.tar.gz Thermolysin] | + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] |
| + | |- | ||
| + | || [http://george.ams.sunysb.edu/SB2010/HIV_PROTEASE.tar.gz HIV Protease] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYbw.png Matrix] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | ||
| + | |- | ||
| + | || [http://george.ams.sunysb.edu/SB2010/NEURAMINIDASE.tar.gz Neuraminidase] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYbw.png Matrix] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | ||
| + | |- | ||
| + | || [http://george.ams.sunysb.edu/SB2010/REVERSE_TRANSCRIPTASE.tar.gz Reverse Transcriptase] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYbw.png Matrix] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | ||
| + | |- | ||
| + | || [http://george.ams.sunysb.edu/SB2010/THERMOLYSIN.tar.gz Thermolysin] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYbw.png Matrix] | ||
| + | || [http://george.ams.sunysb.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYclashes.txt Clash List] | ||
| + | |} | ||
== Sample Docking Results == | == Sample Docking Results == | ||
Revision as of 17:30, 13 September 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 | 2010.09.13_grids.tar.gz |
Note: The energy and bump grids are binary files. These were generated on an Intel Xeon, and should work fine in most cases. Some platforms (e.g. ibm aix) use a different endian ordering and would require the grids to be regenerated.
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. Since energy and bump grids for the aligned receptors are also included, these files are fairly large (300MB-1.4GB).
| Aligned Family | Clash Matrix | Clash List |
|---|---|---|
| Carbonic Anhydrase | Matrix | Clash List |
| HIV Protease | Matrix | Clash List |
| Neuraminidase | Matrix | Clash List |
| Reverse Transcriptase | Matrix | Clash List |
| 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 has been submitted and is currently under review.
Contact Information
Please contact 
if you face any problems.
