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(SB2010 Protein Families [2010.05.19 Initial Release])
 
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== SB2010 Docking Database [2010.05.19 Initial Release]==
+
*[[DGHYD]] Hydration Testset (N=513 systems)
 +
**Database of small molecules with experimental free energies of hydration to test implicit solvation models.  See reference:
 +
**Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory Comput.'', '''2006''', ''2'', 128-139  [http://pubs.acs.org/doi/abs/10.1021/ct050097l]
  
{| 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
 
|-
 
|  Receptors, Ligands and Spheres
 
|| [http://george.ams.sunysb.edu/SB2010/SB2010.05.19_rec.lig.sph.tar.gz 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
 
|| [http://george.ams.sunysb.edu/SB2010/RGD.in RGD] [http://george.ams.sunysb.edu/SB2010/FAD.in FAD] [http://george.ams.sunysb.edu/SB2010/FLX.in FLX]
 
|-
 
|  Flexibility Subset Lists
 
|| [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]
 
|}
 
  
 +
*[[SB2010]] Docking Testset (N=780 systems)
 +
**Database and sample input files to test pose reproduction and crossdocking.  See reference:
 +
**Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. ''J. Chem. Inf. Model'', '''2010''', ''50'', 1986-2000  [http://pubs.acs.org/doi/abs/10.1021/ci1001982]
  
== SB2010 Protein Families [2010.05.19 Initial Release] ==
 
  
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:30%"
+
*[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems)
|- style="background:lightblue; width:10%"
+
**Database and sample input files to test pose reproduction and crossdocking.
! style="width:30%" !| Protein Family
 
! style="width:10%" !| Size
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
 
| 21
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/FACTOR_XA Factor Xa]
 
| 41
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/NEURAMINIDASE Neuraminidase]
 
| 43
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/SIALIDASE Sialidase]
 
| 11
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
 
| 7
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
 
| 7
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
 
| 45
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
 
| 13
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
 
| 29
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/STREPTAVIDIN Streptavidin]
 
| 8
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THROMBIN Thrombin]
 
| 37
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
 
| 20
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
 
| 20
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
 
| 14
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/TRYPSIN Alpha Trypsin]
 
| 46
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/COX COX]
 
| 7
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
 
| 19
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/HIV_PROTEASE HIV Protease]
 
| 60
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THERMOLYSIN Thermolysin]
 
| 26
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
 
| 8
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/MMP Matrix Metalloprotease]
 
| 14
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/LYSOZYME Egg Lysozyme]
 
| 14
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
 
| 15
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
 
| 12
 
|-
 
| [http://george.ams.sunysb.edu/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
 
| 29
 
|}
 
 
 
Please contact [[Image:Sudipto.email.png]] if you face any problems.
 

Latest revision as of 17:29, 20 November 2013

  • DGHYD Hydration Testset (N=513 systems)
    • Database of small molecules with experimental free energies of hydration to test implicit solvation models. See reference:
    • Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory Comput., 2006, 2, 128-139 [1]


  • SB2010 Docking Testset (N=780 systems)
    • Database and sample input files to test pose reproduction and crossdocking. See reference:
    • Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. J. Chem. Inf. Model, 2010, 50, 1986-2000 [2]


  • SB2012 Docking Testset (Expanded version of SB2010, N=1043 systems)
    • Database and sample input files to test pose reproduction and crossdocking.