Difference between revisions of "SB2010"

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(Contact Information)
 
Line 12: Line 12:
 
|-
 
|-
 
|  Receptors, Ligands and Spheres
 
|  Receptors, Ligands and Spheres
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/SB2010.05.19_rec.lig.sph.tar.gz SB2010.05.19_rec.lig.sph.tar.gz]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/SB2010.05.19_rec.lig.sph.tar.gz SB2010.05.19_rec.lig.sph.tar.gz]
 
|-
 
|-
 
|  Energy and Bump Grids
 
|  Energy and Bump Grids
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/2010.09.13_grids.tar.gz 2010.09.13_grids.tar.gz]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/2010.09.13_grids.tar.gz 2010.09.13_grids.tar.gz]
 
|-
 
|-
 
|}
 
|}
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|-
 
|-
 
|  Rigid (RGD)
 
|  Rigid (RGD)
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/RGD.in RGD]  
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/RGD.in RGD]  
 
|-
 
|-
 
|  Fixed Anchor (FAD)
 
|  Fixed Anchor (FAD)
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/FAD.in FAD]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/FAD.in FAD]
 
|-
 
|-
 
|  Flexible Ligand (FLX)
 
|  Flexible Ligand (FLX)
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/FLX.in FLX]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/FLX.in FLX]
 
|}
 
|}
  
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|-
 
|-
 
|  7 or less
 
|  7 or less
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/7orless.txt 7orless]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/7orless.txt 7orless]
 
|-
 
|-
 
|  8 to 15  
 
|  8 to 15  
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/8to15.txt 8to15]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/8to15.txt 8to15]
 
|-
 
|-
 
|  15+  
 
|  15+  
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/15+.txt 15+]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/15+.txt 15+]
 
|-
 
|-
 
|  All Systems
 
|  All Systems
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/all.txt all]  
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/all.txt all]  
 
|}
 
|}
  
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! style="width:10%" !| Size
 
! style="width:10%" !| Size
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
 
| 21
 
| 21
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/FACTOR_XA Factor Xa]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/FACTOR_XA Factor Xa]
 
| 41
 
| 41
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/NEURAMINIDASE Neuraminidase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/NEURAMINIDASE Neuraminidase]
 
| 43
 
| 43
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/SIALIDASE Sialidase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/SIALIDASE Sialidase]
 
| 11
 
| 11
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
 
| 7
 
| 7
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
 
| 7
 
| 7
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
 
| 45
 
| 45
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
 
| 13
 
| 13
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
 
| 29
 
| 29
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/STREPTAVIDIN Streptavidin]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/STREPTAVIDIN Streptavidin]
 
| 8
 
| 8
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/THROMBIN Thrombin]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/THROMBIN Thrombin]
 
| 37
 
| 37
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
 
| 20
 
| 20
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
 
| 20
 
| 20
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
 
| 14
 
| 14
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/TRYPSIN Alpha Trypsin]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/TRYPSIN Alpha Trypsin]
 
| 46
 
| 46
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/COX COX]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/COX COX]
 
| 7
 
| 7
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
 
| 19
 
| 19
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/HIV_PROTEASE HIV Protease]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/HIV_PROTEASE HIV Protease]
 
| 60
 
| 60
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/THERMOLYSIN Thermolysin]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/THERMOLYSIN Thermolysin]
 
| 26
 
| 26
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
 
| 8
 
| 8
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/MMP Matrix Metalloprotease]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/MMP Matrix Metalloprotease]
 
| 14
 
| 14
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/LYSOZYME Egg Lysozyme]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/LYSOZYME Egg Lysozyme]
 
| 14
 
| 14
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
 
| 15
 
| 15
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
 
| 12
 
| 12
 
|-
 
|-
| [http://ringo.ams.sunysb.edu/downloads/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
 
| 29
 
| 29
 
|}
 
|}

Latest revision as of 10:28, 10 June 2019

For more Rizzo Lab downloads: Rizzo Lab Downloads

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.

Sample Docked Poses

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.

MMFF94x Ligands

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.