Difference between revisions of "Rizzo Lab Downloads"

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(→‎SB2010 Protein Families [2010.05.19 Initial Release])
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== 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.  
+
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.  
  
  
−
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:30%"
+
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:60%"
−
|- style="background:lightblue; width:10%"  
+
! style="width:40%" !| Protein Family
−
! style="width:30%" !| 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
 
|}
 
|}
  
 
Please contact [[Image:Sudipto.email.png]] if you face any problems.
 
Please contact [[Image:Sudipto.email.png]] if you face any problems.

Revision as of 16:30, 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. DOCK input files used to evaluate the database are also presented.


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.


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
Aligned Protein Families To be released
Flexible Docked Ensembles To be released
Best Flex Docked Poses To be released
DOCK Sample Inputs RGD FAD FLX
Flexibility Subset Lists 7orless 8to15 15+ 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. 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.


Protein Family Size Clash Subset Aligned Structures
HIV RT 21 To be released To be released
Factor Xa 41 To be released To be released
Neuraminidase 43 To be released To be released
Sialidase 11 To be released To be released
Ribonuclease T1 7 To be released To be released
OMP Decarboxylase 7 To be released To be released
Estrogen Receptor 45 To be released To be released
T4 Lysozyme 13 To be released To be released
Beta Trypsin 29 To be released To be released
Streptavidin 8 To be released To be released
Thrombin 37 To be released To be released
Tyrosine Phosphatase 20 To be released To be released
HMG COA Reductase 20 To be released To be released
Ribonuclease A 14 To be released To be released
Alpha Trypsin 46 To be released To be released
COX 7 To be released To be released
Acetylcholinesterase 19 To be released To be released
HIV Protease 60 To be released To be released
Thermolysin 26 To be released To be released
Carboxypeptidase A 8 To be released To be released
Matrix Metalloprotease 14 To be released To be released
Egg Lysozyme 14 To be released To be released
Phospholipase A2 15 To be released To be released
Thymidylate Synthase 12 To be released To be released
Carbonic Anhydrase 29 To be released To be released

Please contact Sudipto.email.png if you face any problems.

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