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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]
  
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.
 
  
 +
*[[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]
  
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.
 
  
 
+
*[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems)
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
+
**Database and sample input files to test pose reproduction and crossdocking.
|- 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 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.
 
 
 
 
 
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:30%"
 
|- style="background:lightblue; width:10%"
 
! 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.