Difference between revisions of "Rizzo Lab Downloads"

From Rizzo_Lab
Jump to: navigation, search
(→‎SB2010 Protein Families [2010.05.19 Initial Release])
 
(93 intermediate revisions by 5 users not shown)
Line 1: Line 1:
−
== SB2010 Docking Database [2010.05.19 Initial Release]==
 
  
−
{| 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]
 
−
|}
 
  
 +
*[[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]
  
−
== SB2010 Protein Families [2010.05.19 Initial Release] ==
 
  
−
{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:30%"
+
*[[SB2010]] Docking Testset (N=780 systems)
−
|- style="background:lightblue; width:10%"
+
**Database and sample input files to test pose reproduction and crossdocking. See reference:  
−
! style="width:30%" !| Protein Family
+
**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]
−
! 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.
+
 
 +
*[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems)
 +
**Database and sample input files to test pose reproduction and crossdocking.
 +
 
 +
<!-- *[[SB2021.v1]] Docking Testset (Expanded version of SB2021, N=1172 systems) -->
 +
<!--**Database of files required for 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

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"