Difference between revisions of "SB2012"

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For more Rizzo Lab downloads: [[Rizzo Lab Downloads]]
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== SB2012 Docking Database [2012.08.09 Initial Release]==
 
== 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 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. SB2012 is an on-going project.
+
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.  
 +
 
 +
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.
 +
 
 +
SB2012 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://george.ams.sunysb.edu/~fochtman/SB2012.08.09_rec.lig.sph.tar.gz SB2012.08.09_rec.lig.sph.tar.gz]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2012/SB2012.08.09_rec.lig.sph.tar.gz SB2012.08.09_rec.lig.sph.tar.gz]
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|-
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|  Prmtop and Coordinate files for AMBER simulations
 +
|| [https://ringo.ams.stonybrook.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
−
|| [http://george.ams.sunysb.edu/~fochtman/SB2012.08.09_grids.tar.gz 2012.08.09_grids.tar.gz]
+
|| [https://ringo.ams.stonybrook.edu/downloads/SB2012/SB2012.08.09_grids.tar.gz 2012.08.09_grids.tar.gz]
 
|-
 
|-
 +
|  List of all systems (N = 1043)
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2012/clean.systems.all clean.systems.all]
 
|}
 
|}
  
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== DOCK Input Files ==
 
== DOCK Input Files ==
  
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These are the DOCK input files used to evaluate the database.
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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%"
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|- style="background:lightblue"
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! style="width:50%" !|Resource
 +
! style="width:50%" !|Filename
 +
|-
 +
|  Rigid (RGD)
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/RGD.in RGD]
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|-
 +
|  Fixed Anchor (FAD)
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/FAD.in FAD]
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|-
 +
|  Flexible Ligand (FLX)
 +
|| [https://ringo.ams.stonybrook.edu/downloads/SB2010/FLX.in FLX]
 +
|}
 +
 
 +
These are the input files used to evaluate the database for '''DOCK6.8''' (releasing soon).
  
 
{| 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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|-
 
|-
 
|  Rigid (RGD)
 
|  Rigid (RGD)
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|| [http://george.ams.sunysb.edu/SB2010/RGD.in RGD]
+
|| Coming Soon
 
|-
 
|-
 
|  Fixed Anchor (FAD)
 
|  Fixed Anchor (FAD)
−
|| [http://george.ams.sunysb.edu/SB2010/FAD.in FAD]
+
|| Coming Soon
 
|-
 
|-
 
|  Flexible Ligand (FLX)
 
|  Flexible Ligand (FLX)
−
|| [http://george.ams.sunysb.edu/SB2010/FLX.in FLX]
+
|| Coming Soon
 
|}
 
|}
  
−
== SB2012 Ligand Flexibility Subsets - Coming Soon ==
+
== SB2012 Ligand Flexibility Subsets ==
  
 +
Here are text files of systems in the database broken up by number of rotatable bonds. (As interpreted by DOCK.)
  
−
== SB2012 Protein Families - Coming Soon ==
+
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
 +
|- style="background:lightblue"
 +
! style="width:50%" !|Resource
 +
! style="width:50%" !|Filename
 +
|-
 +
|  7 or less
 +
|| [https://ringo.ams.stonybrook.edu/downloads/SB2012/rotbonds/7orless.rotbonds 7orless]
 +
|-
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|  8 to 15
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|| [https://ringo.ams.stonybrook.edu/downloads/SB2012/rotbonds/8to15.rotbonds 8to15]
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|-
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|  >15
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|| [https://ringo.ams.stonybrook.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
 +
 +
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/ACETYLCHOLINESTERASE ACETYLCHOLINESTERASE] N= 19
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/BETA-TRYPSIN BETA-TRYPSIN] N= 29
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/CARBONIC_ANHYDRASE CARBONIC_ANHYDRASE] N= 29
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/CARBOXYPEPTIDASE_A CARBOXYPEPTIDASE_A] N= 8
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/COX COX] N= 7
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/ESTROGEN_RECEPTOR ESTROGEN_RECEPTOR] N= 45
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/FACTOR_XA FACTOR_XA] N= 41
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/HIV_PROTEASE HIV_PROTEASE] N= 60
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/HMG_COA_REDUCTASE HMG_COA_REDUCTASE] N= 20
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/LYSOZYME LYSOZYME] N= 14
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/MISC_FAMILIES MISC_FAMILIES] N= 214
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/MMP MMP] N= 14
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/NEURAMINIDASE NEURAMINIDASE] N= 43
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/OMP_DECARBOXYLASE OMP_DECARBOXYLASE] N= 7
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/PHOSPHOLIPASE_A2 PHOSPHOLIPASE_A2] N= 15
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/REVERSE_TRANSCRIPTASE REVERSE_TRANSCRIPTASE] N= 21
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|-
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| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/RIBONUCLEASE_A RIBONUCLEASE_A] N= 14
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|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/RIBONUCLEASE_T1 RIBONUCLEASE_T1] N= 7
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|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/SIALIDASE SIALIDASE] N= 11
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|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/STREPTAVIDIN STREPTAVIDIN] N= 8
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/T4_LYSOZYME T4_LYSOZYME] N= 13
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|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/THERMOLYSIN THERMOLYSIN] N= 26
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/THROMBIN THROMBIN] N= 37
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/THYMIDYLATE_SYNTHASE THYMIDYLATE_SYNTHASE] N= 12
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/TRYPSIN TRYPSIN] N= 46
 +
|-
 +
| [https://ringo.ams.stonybrook.edu/downloads/SB2012/families.large/TYROSINE_PHOSPHATASE TYROSINE_PHOSPHATASE] N= 20
 +
|}
  
 
== Aligned Families - Coming Soon ==
 
== Aligned Families - Coming Soon ==
  
  
−
== Sample Docking Results - 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.
  
 +
[https://ringo.ams.stonybrook.edu/downloads/SB2012/sample_docking_results.tar sample_docking_results.tar]
  
 
== Copyright ==
 
== 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 has been accepted and is currently in press.
+
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 ==
 
== Contact Information ==
−
Please contact [[Image:Brian_email.png]] if you face any problems. <BR>
+
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.
 
Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.

Latest revision as of 13:56, 30 August 2023

For more Rizzo Lab downloads: Rizzo Lab Downloads

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 protein-ligand 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.

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.

SB2012 is an on-going project.

Resource Filename
Receptors, Ligands and Spheres SB2012.08.09_rec.lig.sph.tar.gz
Prmtop and Coordinate files for AMBER simulations SB2012.08.09_rec.lig.pro.com_amber.tar.gz
Energy and Bump Grids 2012.08.09_grids.tar.gz
List of all systems (N = 1043) clean.systems.all

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 input files used to evaluate the database for DOCK6.7.

Resource Filename
Rigid (RGD) RGD
Fixed Anchor (FAD) FAD
Flexible Ligand (FLX) FLX

These are the input files used to evaluate the database for DOCK6.8 (releasing soon).

Resource Filename
Rigid (RGD) Coming Soon
Fixed Anchor (FAD) Coming Soon
Flexible Ligand (FLX) Coming Soon

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. (Only targets with <=7 structures are shown.)

Resource


ACETYLCHOLINESTERASE N= 19
BETA-TRYPSIN 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

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.

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 "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.

Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=SB2012&oldid=16368"