Difference between revisions of "Rizzo Lab Downloads"

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(→‎SB2010 Docking Database [2010.05.19 Initial Release])
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== SB2010 Docking Database [2010.05.19 Initial Release]==
 
== 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. DOCK input files used to evaluate the database are also presented.
+
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.  
  
  
−
The '''Flexibility Subset Lists''' divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges. Brackets marked as 'To be released' will be made available as the relevant manuscripts are submitted. SB2010 is an on-going project; more structures and related resources will be added in the future. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.
+
SB2010 is an on-going project; more structures and related resources will be added in the future. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.
  
  
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|-
 
|-
 
|  Alternate Ligand Charge Models
 
|  Alternate Ligand Charge Models
−
|| To be released
 
−
|-
 
−
|  Aligned Protein Families
 
−
|| To be released
 
−
|-
 
−
|  Flexible Docked Ensembles
 
 
|| To be released
 
|| To be released
 
|-
 
|-
 
|  Best Flex Docked Poses
 
|  Best Flex Docked Poses
−
|| To be released
 
−
|-
 
−
|  Unbiased Ligand Structures
 
 
|| To be released
 
|| To be released
 
|-
 
|-
Line 39: Line 30:
 
|| [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless] [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15] [http://george.ams.sunysb.edu/SB2010/15+.txt 15+] [http://george.ams.sunysb.edu/SB2010/all.txt all]  
 
|| [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless] [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15] [http://george.ams.sunysb.edu/SB2010/15+.txt 15+] [http://george.ams.sunysb.edu/SB2010/all.txt all]  
 
|}
 
|}
 +
 +
 +
== DOCK Input Files ==
 +
 +
These are the DOCK input files used to evaluate the database.
 +
 +
{| 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
 +
|-
 +
|  Rigid (RGD)
 +
|| [http://george.ams.sunysb.edu/SB2010/RGD.in RGD]
 +
|-
 +
|  Fixed Anchor (FAD)
 +
|| [http://george.ams.sunysb.edu/SB2010/FAD.in FAD]
 +
|-
 +
|  Flexible Ligand (FLX)
 +
|| [http://george.ams.sunysb.edu/SB2010/FLX.in 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.
 +
 +
{| 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
 +
|| [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless]
 +
|-
 +
|  8 to 15
 +
|| [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15]
 +
|-
 +
|  15+
 +
|| [http://george.ams.sunysb.edu/SB2010/15+.txt 15+]
 +
|-
 +
|  All Systems
 +
|| [http://george.ams.sunysb.edu/SB2010/all.txt all]
 +
|}
 +
  
 
== SB2010 Protein Families [2010.05.19 Initial Release] ==
 
== 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. Clash subset indicates a subset of each protein family where inter-molecular clashes exist, which could possibly be resolved with flexible receptor docking. Aligned Structures contain the receptor and ligand mol2 files aligned to the first receptor in each family.  
+
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.  
  
  
−
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:80%"
+
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:50%"
 
! style="width:40%" !| Protein Family
 
! style="width:40%" !| Protein Family
 
! style="width:10%" !| Size
 
! style="width:10%" !| Size
−
! style="width:25%" !| Clash Subset
 
−
! style="width:25%" !| Aligned Structures
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
 
| 21
 
| 21
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/FACTOR_XA Factor Xa]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/FACTOR_XA Factor Xa]
 
| 41
 
| 41
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/NEURAMINIDASE Neuraminidase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/NEURAMINIDASE Neuraminidase]
 
| 43
 
| 43
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/SIALIDASE Sialidase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/SIALIDASE Sialidase]
 
| 11
 
| 11
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
 
| 7
 
| 7
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
 
| 7
 
| 7
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
 
| 45
 
| 45
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
 
| 13
 
| 13
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
 
| 29
 
| 29
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/STREPTAVIDIN Streptavidin]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/STREPTAVIDIN Streptavidin]
 
| 8
 
| 8
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THROMBIN Thrombin]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THROMBIN Thrombin]
 
| 37
 
| 37
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
 
| 20
 
| 20
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
 
| 20
 
| 20
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
 
| 14
 
| 14
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TRYPSIN Alpha Trypsin]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TRYPSIN Alpha Trypsin]
 
| 46
 
| 46
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/COX COX]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/COX COX]
 
| 7
 
| 7
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
 
| 19
 
| 19
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HIV_PROTEASE HIV Protease]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HIV_PROTEASE HIV Protease]
 
| 60
 
| 60
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THERMOLYSIN Thermolysin]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THERMOLYSIN Thermolysin]
 
| 26
 
| 26
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
 
| 8
 
| 8
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/MMP Matrix Metalloprotease]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/MMP Matrix Metalloprotease]
 
| 14
 
| 14
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/LYSOZYME Egg Lysozyme]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/LYSOZYME Egg Lysozyme]
 
| 14
 
| 14
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
 
| 15
 
| 15
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
 
| 12
 
| 12
−
| To be released
 
−
| To be released
 
 
|-
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
 
| 29
 
| 29
−
| To be released
 
−
| To be released
 
 
|}
 
|}
  

Revision as of 16:53, 20 July 2010

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. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.


Resource Filename
Receptors, Ligands and Spheres SB2010.05.19_rec.lig.sph.tar.gz
Energy and Bump Grids To be released
Alternate Ligand Charge Models To be released
Best Flex Docked Poses To be released
DOCK Sample Inputs RGD FAD FLX
Flexibility Subset Lists 7orless 8to15 15+ all


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


Copyright

This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useably 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 Sudipto.email.png if you face any problems.

Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=Rizzo_Lab_Downloads&oldid=5853"