Difference between revisions of "SB2021.v1"

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For more Rizzo Lab downloads: [[Rizzo Lab Downloads]]  
 
For more Rizzo Lab downloads: [[Rizzo Lab Downloads]]  
  
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== SB2012 Docking Database [2012.08.09 Initial Release]==
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== SB2021 Docking Database [2021.11.19 Initial Release]==
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SB2012 is an updated release of the [[SB2010]] docking validation database. The database has been updated to contain ~1000 protein-ligand complexes including several new protein families. Please refer to the publication [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "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.  
+
SB2021 is an updated release of the SB2012 docking validation database. The database has been updated to contain 1,172 protein-ligand complexes including addition protein structures bound to approved drug molecules, and new/ expanded sets of crossdocking families. Additionally 5 systems formerly in SB2012 have been removed as they did not align with the high quality standards of the set. Please refer to the publication [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "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.  
  
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For the prmtop and coordinate files, the nomenclature is as follows: ORI = Original Crystal Structure Coordinates, COM = Complex (REC + LIG), PRO = Protein Only, REC = Protein and any included Cofactors, LIG = Ligand.
 
  
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SB2012 is an on-going project.
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SB2021 is an on-going project.
  
 
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
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|-
 
|-
 
|  Receptors, Ligands and Spheres
 
|  Receptors, Ligands and Spheres
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/SB2012.08.09_rec.lig.sph.tar.gz SB2012.08.09_rec.lig.sph.tar.gz]
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2021/2021_11_19.lig_rec_sph.tar.gz 2021_11_19.lig_rec_sph.tar.gz]
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|-
 
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|  Prmtop and Coordinate files for AMBER simulations
 
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/SB2012.08.09_rec.lig.pro.com_amber.tar.gz SB2012.08.09_rec.lig.pro.com_amber.tar.gz]
 
 
|-
 
|-
 
|  Energy and Bump Grids
 
|  Energy and Bump Grids
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/SB2012.08.09_grids.tar.gz 2012.08.09_grids.tar.gz]
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2021/2021_11_19.grid_files.tar.gz 2021_11_19.grid_files.tar.gz]
 
|-
 
|-
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|  List of all systems (N = 1043)
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|  List of all systems (N = 1,172)
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/clean.systems.all clean.systems.all]
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2021/clean.systems.all clean.systems.all]
 
|}
 
|}
  
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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.
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== SB2021 Protein Families ==
  
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== DOCK Input Files ==
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Here are text files of systems in the database broken up by protein target.  
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+
(Only targets with <=8 structures are shown.)
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These are the input files used to evaluate the database for '''DOCK6.7'''.
 
  
 
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
|- style="background:lightblue"
 
|- style="background:lightblue"
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! style="width:50%" !|Resource
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! style="width:100%" !|Resource
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! style="width:50%" !|Filename
 
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|-
 
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|  Rigid (RGD)
 
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|| [http://ringo.ams.sunysb.edu/downloads/SB2010/RGD.in RGD]
 
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|-
 
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|  Fixed Anchor (FAD)
 
−
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/FAD.in FAD]
 
−
|-
 
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|  Flexible Ligand (FLX)
 
−
|| [http://ringo.ams.sunysb.edu/downloads/SB2010/FLX.in FLX]
 
−
|}
 
  
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These are the input files used to evaluate the database for '''DOCK6.8''' (releasing soon).
 
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−
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
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|- style="background:lightblue"
 
−
! style="width:50%" !|Resource
 
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! style="width:50%" !|Filename
 
−
|-
 
−
|  Rigid (RGD)
 
−
|| Coming Soon
 
 
|-
 
|-
−
| Fixed Anchor (FAD)
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/ABL_Kinase.txt ABL_Kinase] N= 24
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|| Coming Soon
 
 
|-
 
|-
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| Flexible Ligand (FLX)
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Acetylcholinesterase.txt Acetylcholinesterase] N= 20
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|| Coming Soon
 
−
|}
 
−
 
 
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== SB2012 Ligand Flexibility Subsets ==
 
−
 
 
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Here are text files of systems in the database broken up by number of rotatable bonds. (As interpreted by DOCK.)
 
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{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
−
|- style="background:lightblue"
 
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! style="width:50%" !|Resource
 
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! style="width:50%" !|Filename
 
 
|-
 
|-
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|  7 or less
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Adenosine_Deaminase.txt Adenosine_Deaminase] N= 8
−
|| [http://ringo.ams.sunysb.edu/downloads/SB2012/rotbonds/7orless.rotbonds 7orless]  
 
 
|-
 
|-
−
|  8 to 15
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Beta_Trypsin.txt Beta_Trypsin] N= 29
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/rotbonds/8to15.rotbonds 8to15]
 
 
|-
 
|-
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|  >15
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Carbonic_Anhydrase.txt Carbonic_Anhydrase] N= 31
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|| [http://ringo.ams.sunysb.edu/downloads/SB2012/rotbonds/15+rotbonds 15+]
 
−
|}
 
−
 
 
−
== SB2012 Protein Families ==
 
−
 
 
−
Here are text files of systems in the database broken up by protein target.
 
−
(Only targets with <=7 structures are shown.)
 
−
 
 
−
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 
−
|- style="background:lightblue"
 
−
! style="width:100%" !|Resource
 
−
 
 
−
 
 
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/ACETYLCHOLINESTERASE ACETYLCHOLINESTERASE] N= 19
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Carboxypeptidase_A.txt Carboxypeptidase_A] N= 8
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/BETA-TRYPSIN BETA-TRYPSIN] N= 29
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/CDK.txt CDK] N= 10
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/CARBONIC_ANHYDRASE CARBONIC_ANHYDRASE] N= 29
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Coagulation_Factor_Xa.txt Coagulation_Factor_Xa] N= 43
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/CARBOXYPEPTIDASE_A CARBOXYPEPTIDASE_A] N= 8
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/COX.txt COX] N= 9
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/COX COX] N= 7
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| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/EGFR.txt EGFR] N= 15
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/ESTROGEN_RECEPTOR ESTROGEN_RECEPTOR] N= 45
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Estrogen_Receptor.txt Estrogen_Receptor] N= 47
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/FACTOR_XA FACTOR_XA] N= 41
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/HIV_Protease.txt HIV_Protease] N= 66
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/HIV_PROTEASE HIV_PROTEASE] N= 60
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/HIV_Reverse_Transcriptase.txt HIV_Reverse_Transcriptase] N= 27
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/HMG_COA_REDUCTASE HMG_COA_REDUCTASE] N= 20
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/HMG_CoA_Reductase.txt HMG_CoA_Reductase] N= 19
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/LYSOZYME LYSOZYME] N= 14
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Hsp_90.txt Hsp_90] N= 13
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/MISC_FAMILIES MISC_FAMILIES] N= 214
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/IGF1_R.txt IGF1_R] N= 9
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/MMP MMP] N= 14
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/LpxC.txt LpxC] N= 33
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/NEURAMINIDASE NEURAMINIDASE] N= 43
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Lysozyme.txt Lysozyme] N= 14
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/OMP_DECARBOXYLASE OMP_DECARBOXYLASE] N= 7
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/MMP.txt MMP] N= 16
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/PHOSPHOLIPASE_A2 PHOSPHOLIPASE_A2] N= 15
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Neuraminidase.txt Neuraminidase] N= 44
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/REVERSE_TRANSCRIPTASE REVERSE_TRANSCRIPTASE] N= 21
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Phosphodiesterase.txt Phosphodiesterase] N= 17
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/RIBONUCLEASE_A RIBONUCLEASE_A] N= 14
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/PPAR_Kinase.txt PPAR_Kinase] N= 21
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/RIBONUCLEASE_T1 RIBONUCLEASE_T1] N= 7
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Protein_Tyrosine_Phosphatase.txt Protein_Tyrosine_Phosphatase] N= 20
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/SIALIDASE SIALIDASE] N= 11
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Ribonuclease_A.txt Ribonuclease_A] N= 14
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/STREPTAVIDIN STREPTAVIDIN] N= 8
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Streptavidin.txt Streptavidin] N= 8
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/T4_LYSOZYME T4_LYSOZYME] N= 13
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/T4_Lysozyme.txt T4_Lysozyme] N= 13
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THERMOLYSIN THERMOLYSIN] N= 26
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Thermolysin.txt Thermolysin] N= 26
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THROMBIN THROMBIN] N= 37
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Thrombin.txt Thrombin] N= 40
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/THYMIDYLATE_SYNTHASE THYMIDYLATE_SYNTHASE] N= 12
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Thymidylate_Synthase.txt Thymidylate_Synthase] N= 14
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/TRYPSIN TRYPSIN] N= 46
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Trypsin.txt Trypsin] N= 46
 
|-
 
|-
−
| [http://ringo.ams.sunysb.edu/downloads/SB2012/families.large/TYROSINE_PHOSPHATASE TYROSINE_PHOSPHATASE] N= 20
+
| [https://ringo.ams.stonybrook.edu/downloads/SB2021/zzz.Family_Information/Vitamin_D_Nuclear_Receptor.txt Vitamin_D_Nuclear_Receptor] N= 38
−
|}
 
−
 
 
−
== Aligned Families - Coming Soon ==
 
−
 
 
−
 
 
−
== Sample Docking Results ==
 
−
The link below contains sample docking results using the standard FLX protocol for all systems in the testset.  These results were published in ''paper in press''.  While these results are representative, DOCK relies on stochastic minimization so your results may vary.
 
−
 
 
−
[http://ringo.ams.sunysb.edu/downloads/SB2012/sample_docking_results.tar sample_docking_results.tar]
 
−
 
 
−
== 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 [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "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 [[Rizzo Lab Members and Contact Information|here]]. <BR>
 
−
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.
 

Latest revision as of 13:55, 30 August 2023

For more Rizzo Lab downloads: Rizzo Lab Downloads

SB2021 Docking Database [2021.11.19 Initial Release]

SB2021 is an updated release of the SB2012 docking validation database. The database has been updated to contain 1,172 protein-ligand complexes including addition protein structures bound to approved drug molecules, and new/ expanded sets of crossdocking families. Additionally 5 systems formerly in SB2012 have been removed as they did not align with the high quality standards of the set. 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.


SB2021 is an on-going project.

Resource Filename
Receptors, Ligands and Spheres 2021_11_19.lig_rec_sph.tar.gz
Energy and Bump Grids 2021_11_19.grid_files.tar.gz
List of all systems (N = 1,172) clean.systems.all

SB2021 Protein Families

Here are text files of systems in the database broken up by protein target. (Only targets with <=8 structures are shown.)

Resource
ABL_Kinase N= 24
Acetylcholinesterase N= 20
Adenosine_Deaminase N= 8
Beta_Trypsin N= 29
Carbonic_Anhydrase N= 31
Carboxypeptidase_A N= 8
CDK N= 10
Coagulation_Factor_Xa N= 43
COX N= 9
EGFR N= 15
Estrogen_Receptor N= 47
HIV_Protease N= 66
HIV_Reverse_Transcriptase N= 27
HMG_CoA_Reductase N= 19
Hsp_90 N= 13
IGF1_R N= 9
LpxC N= 33
Lysozyme N= 14
MMP N= 16
Neuraminidase N= 44
Phosphodiesterase N= 17
PPAR_Kinase N= 21
Protein_Tyrosine_Phosphatase N= 20
Ribonuclease_A N= 14
Streptavidin N= 8
T4_Lysozyme N= 13
Thermolysin N= 26
Thrombin N= 40
Thymidylate_Synthase N= 14
Trypsin N= 46
Vitamin_D_Nuclear_Receptor N= 38
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