Difference between revisions of "SB2012"
(→SB2012 Ligand Flexibility Subsets) 
(→SB2012 Protein Families  Coming Soon) 

Line 58:  Line 58:  
}  }  
−  == SB2012 Protein Families  +  == SB2012 Protein Families == 
+  Here are text files of systems in the database broken up by protein target.  
+  
+  { border="1" cellpadding="8" cellspacing="0" style="background:white; textalign:left; width:60%"  
+   style="background:lightblue"  
+  ! style="width:100%" !Resource  
+  
+  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/ACETYLCHOLINESTERASE ACETYLCHOLINESTERASE] N= 19  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/BETATRYPSIN BETATRYPSIN] N= 29  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/CARBONIC_ANHYDRASE CARBONIC_ANHYDRASE] N= 29  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/CARBOXYPEPTIDASE_A CARBOXYPEPTIDASE_A] N= 8  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/COX COX] N= 7  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/ESTROGEN_RECEPTOR ESTROGEN_RECEPTOR] N= 45  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/FACTOR_XA FACTOR_XA] N= 41  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/HIV_PROTEASE HIV_PROTEASE] N= 60  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/HMG_COA_REDUCTASE HMG_COA_REDUCTASE] N= 20  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/LYSOZYME LYSOZYME] N= 14  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/MISC_FAMILIES MISC_FAMILIES] N= 214  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/MMP MMP] N= 14  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/NEURAMINIDASE NEURAMINIDASE] N= 43  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/OMP_DECARBOXYLASE OMP_DECARBOXYLASE] N= 7  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/PHOSPHOLIPASE_A2 PHOSPHOLIPASE_A2] N= 15  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/REVERSE_TRANSCRIPTASE REVERSE_TRANSCRIPTASE] N= 21  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/RIBONUCLEASE_A RIBONUCLEASE_A] N= 14  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/RIBONUCLEASE_T1 RIBONUCLEASE_T1] N= 7  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/SIALIDASE SIALIDASE] N= 11  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/STREPTAVIDIN STREPTAVIDIN] N= 8  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/T4_LYSOZYME T4_LYSOZYME] N= 13  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THERMOLYSIN THERMOLYSIN] N= 26  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THROMBIN THROMBIN] N= 37  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THYMIDYLATE_SYNTHASE THYMIDYLATE_SYNTHASE] N= 12  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/TRYPSIN TRYPSIN] N= 46  
+    
+   [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/TYROSINE_PHOSPHATASE TYROSINE_PHOSPHATASE] N= 20  
+  }  
== Aligned Families  Coming Soon ==  == Aligned Families  Coming Soon == 
Revision as of 15:08, 14 April 2015
For more Rizzo Lab downloads: Rizzo Lab Downloads
Contents
SB2012 Docking Database [2012.08.09 Initial Release]
SB2012 is an updated release of the SB2010 docking validation database. The database has been updated to contain ~1000 proteinligand complexes including several new protein families. Please refer to the publication "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments" for information regarding structure preparation. 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. SB2012 is an ongoing project.
Resource  Filename 

Receptors, Ligands and Spheres  SB2012.08.09_rec.lig.sph.tar.gz 
Energy and Bump Grids  2012.08.09_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 
SB2012 Ligand Flexibility Subsets
Here are text files of systems in the database broken up by number of rotatable bonds. (As interpreted by DOCK.)
Resource  Filename 

7 or less  7orless 
8 to 15  8to15 
>15  15+ 
SB2012 Protein Families
Here are text files of systems in the database broken up by protein target.
Resource


ACETYLCHOLINESTERASE N= 19 
BETATRYPSIN N= 29 
CARBONIC_ANHYDRASE N= 29 
CARBOXYPEPTIDASE_A N= 8 
COX N= 7 
ESTROGEN_RECEPTOR N= 45 
FACTOR_XA N= 41 
HIV_PROTEASE N= 60 
HMG_COA_REDUCTASE N= 20 
LYSOZYME N= 14 
MISC_FAMILIES N= 214 
MMP N= 14 
NEURAMINIDASE N= 43 
OMP_DECARBOXYLASE N= 7 
PHOSPHOLIPASE_A2 N= 15 
REVERSE_TRANSCRIPTASE N= 21 
RIBONUCLEASE_A N= 14 
RIBONUCLEASE_T1 N= 7 
SIALIDASE N= 11 
STREPTAVIDIN N= 8 
T4_LYSOZYME N= 13 
THERMOLYSIN N= 26 
THROMBIN N= 37 
THYMIDYLATE_SYNTHASE N= 12 
TRYPSIN N= 46 
TYROSINE_PHOSPHATASE N= 20 
Aligned Families  Coming Soon
Sample Docking Results  Coming Soon
Copyright
This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely usable 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 if you face any problems.
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.