Difference between revisions of "Rizzo Lab Downloads"

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== SB2010 Docking Database [2010.05.19 Initial Release]==
 
  
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{| 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
 
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! style="width:50%" !|Filename
 
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|-
 
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|  Receptors, Ligands and Spheres
 
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|| [http://george.ams.sunysb.edu/SB2010/SB2010.05.19_rec.lig.sph.tar.gz SB2010.05.19_rec.lig.sph.tar.gz]
 
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|-
 
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|  Energy and Bump Grids
 
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|| To be released
 
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|-
 
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|  Alternate Ligand Charge Models
 
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|| To be released
 
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|-
 
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|  Aligned Protein Families
 
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|| To be released
 
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|-
 
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|  DOCK Sample Inputs
 
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|| [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]
 
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|-
 
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|  Flexibility Subset Lists
 
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|| [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+]
 
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|}
 
  
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Please contact [[Image:Sudipto.email.png]] if you face any problems.
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*[[DGHYD]] Hydration Testset (N=513 systems)
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**Database of small molecules with experimental free energies of hydration to test implicit solvation models.  See reference:
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**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]
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*[[SB2010]] Docking Testset (N=780 systems)
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**Database and sample input files to test pose reproduction and crossdocking.  See reference:
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**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]
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*[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems)
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**Database and sample input files to test pose reproduction and crossdocking.
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<!-- *[[SB2021.v1]] Docking Testset (Expanded version of SB2021, N=1172 systems) -->
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<!--**Database of files required for pose reproduction and crossdocking.-->
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For lab members: The path to upload downloadable files on the Ringo server is found at
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/export/home/Downloads_path.txt

Latest revision as of 12:52, 19 February 2024


  • 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.


For lab members: The path to upload downloadable files on the Ringo server is found at 

/export/home/Downloads_path.txt
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=Rizzo_Lab_Downloads&oldid=16756"