Difference between revisions of "Rizzo Lab Downloads"

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Latest Release:  [[SB2012]]
 
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SB2012 Docking Database [[SB2012]]
 
  
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SB2012 Docking Database [[SB2010]]
 
  
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*[[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]
  
  
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== SB2010 Docking Database [2010.05.19 Initial Release]==
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*[[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]
  
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The downloads presented here refer to the publication [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments"]. 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. SB2010 is an on-going project; more structures and related resources will be added in the future. Work on [[SB2011 testset]] release is in progress.
 
  
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{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%"
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*[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems)
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|- style="background:lightblue"
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**Database and sample input files to test pose reproduction and crossdocking.
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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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|| [http://george.ams.sunysb.edu/SB2010/2010.09.13_grids.tar.gz 2010.09.13_grids.tar.gz]
 
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|-
 
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|}
 
  
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Note: The DOCK energy and bump grids provided are binary files (13GB download). These were generated on an Intel Xeon, and should work fine with DOCK 4 or greater. Some platforms (e.g. ibm aix) use a different endian ordering and would require the grids to be regenerated. The grids are provided for convenience, and can be generated independently from the receptor files. The receptor and ligand mol2 files should also be compatible with most other commercial and academic docking programs. If you would like to suggest alternative file formats (pdb,sdf etc) to facilitate use with a particular tool, please contact the authors.
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<!-- *[[SB2021.v1]] Docking Testset (Expanded version of SB2021, N=1172 systems) -->
 +
<!--**Database of files required for pose reproduction and crossdocking.-->
  
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== DOCK Input Files ==
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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
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These are the DOCK input files used to evaluate the database.
 
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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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|  Rigid (RGD)
 
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|| [http://george.ams.sunysb.edu/SB2010/RGD.in RGD]
 
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|-
 
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|  Fixed Anchor (FAD)
 
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|| [http://george.ams.sunysb.edu/SB2010/FAD.in FAD]
 
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|-
 
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|  Flexible Ligand (FLX)
 
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|| [http://george.ams.sunysb.edu/SB2010/FLX.in FLX]
 
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|}
 
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== SB2010 Ligand Flexibility Subsets ==
 
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The '''Flexibility Subset Lists''' divide the database into three subsets to allow benchmarking of docking programs across three ligand flexibility ranges.
 
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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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|  7 or less
 
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|| [http://george.ams.sunysb.edu/SB2010/7orless.txt 7orless]
 
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|-
 
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|  8 to 15
 
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|| [http://george.ams.sunysb.edu/SB2010/8to15.txt 8to15]
 
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|-
 
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|  15+
 
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|| [http://george.ams.sunysb.edu/SB2010/15+.txt 15+]
 
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|-
 
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|  All Systems
 
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|| [http://george.ams.sunysb.edu/SB2010/all.txt all]
 
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|}
 
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== SB2010 Protein Families [2010.05.19 Initial Release] ==
 
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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.
 
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{| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:50%"
 
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! style="width:40%" !| Protein Family
 
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! style="width:10%" !| Size
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/REVERSE_TRANSCRIPTASE HIV RT]
 
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| 21
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/FACTOR_XA Factor Xa]
 
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| 41
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/NEURAMINIDASE Neuraminidase]
 
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| 43
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/SIALIDASE Sialidase]
 
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| 11
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_T1 Ribonuclease T1]
 
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| 7
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/OMP_DECARBOXYLASE OMP Decarboxylase]
 
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| 7
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/ESTROGEN_RECEPTOR Estrogen Receptor]
 
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| 45
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/T4_LYSOZYME T4 Lysozyme]
 
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| 13
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/BETA-TRYPSIN Beta Trypsin]
 
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| 29
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/STREPTAVIDIN Streptavidin]
 
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| 8
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/THROMBIN Thrombin]
 
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| 37
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/TYROSINE_PHOSPHATASE Tyrosine Phosphatase]
 
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| 20
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/HMG_COA_REDUCTASE HMG COA Reductase]
 
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| 20
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/RIBONUCLEASE_A Ribonuclease A]
 
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| 14
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/TRYPSIN Alpha Trypsin]
 
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| 46
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/COX COX]
 
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| 7
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/ACETYLCHOLINESTERASE Acetylcholinesterase]
 
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| 19
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/HIV_PROTEASE HIV Protease]
 
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| 60
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/THERMOLYSIN Thermolysin]
 
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| 26
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/CARBOXYPEPTIDASE_A Carboxypeptidase A]
 
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| 8
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/MMP Matrix Metalloprotease]
 
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| 14
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/LYSOZYME Egg Lysozyme]
 
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| 14
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/PHOSPHOLIPASE_A2 Phospholipase A2]
 
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| 15
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/THYMIDYLATE_SYNTHASE Thymidylate Synthase]
 
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| 12
 
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|-
 
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| [http://george.ams.sunysb.edu/SB2010/families.large/CARBONIC_ANHYDRASE Carbonic Anhydrase]
 
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| 29
 
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|}
 
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== Aligned Families ==
 
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Alignment for 5 protein families are presented. Each receptor was aligned to the first PDB code in the corresponding family list above. The same transformation was then applied to the ligand. The Aligned Family column has only the aligned receptor and ligand files. Pre-computed DOCK energy and bump grids (300MB-1.4GB for each set) are also available for the aligned families in the "Family+Grids" column.
 
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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:25%" !|Aligned Family
 
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! style="width:25%" !|Family+Grids
 
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! style="width:25%" !|Clash Matrix
 
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! style="width:25%" !|Clash List
 
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|-
 
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|| [http://george.ams.sunysb.edu/SB2010/CARBONIC_ANHYDRASE_rec.lig.tar.gz Carbonic Anhydrase]
 
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|| [http://george.ams.sunysb.edu/SB2010/CARBONIC_ANHYDRASE.tar.gz Carbonic Anhydrase]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYbw.png Matrix]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/CARBONIC_ANHYDRASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List]
 
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|-
 
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|| [http://george.ams.sunysb.edu/SB2010/HIV_PROTEASE_rec.lig.tar.gz HIV Protease]
 
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|| [http://george.ams.sunysb.edu/SB2010/HIV_PROTEASE.tar.gz HIV Protease]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYbw.png Matrix]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/HIV_PROTEASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List] 
 
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|-
 
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|| [http://george.ams.sunysb.edu/SB2010/NEURAMINIDASE_rec.lig.tar.gz Neuraminidase] 
 
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|| [http://george.ams.sunysb.edu/SB2010/NEURAMINIDASE.tar.gz Neuraminidase] 
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYbw.png Matrix]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/NEURAMINIDASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List]
 
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|-
 
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|| [http://george.ams.sunysb.edu/SB2010/REVERSE_TRANSCRIPTASE_rec.lig.tar.gz Reverse Transcriptase]  
 
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|| [http://george.ams.sunysb.edu/SB2010/REVERSE_TRANSCRIPTASE.tar.gz Reverse Transcriptase] 
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYbw.png Matrix]
 
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|| [http://george.ams.sunysb.edu/SB2010/families.clashes/REVERSE_TRANSCRIPTASExtalmin.1000iter-tether10ENERGYclashes.txt Clash List]
 
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|-
 
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|| [http://george.ams.sunysb.edu/SB2010/THERMOLYSIN_rec.lig.tar.gz Thermolysin]
 
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|| [http://george.ams.sunysb.edu/SB2010/THERMOLYSIN.tar.gz Thermolysin]
 
−
|| [http://george.ams.sunysb.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYbw.png Matrix]
 
−
|| [http://george.ams.sunysb.edu/SB2010/families.clashes/THERMOLYSINxtalmin.1000iter-tether10ENERGYclashes.txt Clash List]
 
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|}
 
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== Sample Docking Results ==
 
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Sample docking results with the top scored pose for each pdb code. These results were produced with DOCK 6.4, using the dock input files shown above. Please note that you will get slightly different results, depending on the environment you use to compile the dock binaries.
 
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[http://george.ams.sunysb.edu/SB2010/2010.08.09_top_scored_poses.tar.gz Sample Docked Poses]
 
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== Alternative Ligand Starting Geometries ==
 
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XXXX.lig.mmff94x_gasmin.mol2 are alternative initial ligand coordinates obtained from gas-phase minimization (in absence of the receptor) with the MMFF94x forcefield with the MOE 2009.10 program. MMFF94x charges are assigned to the ligands before minimization.
 
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[http://george.ams.sunysb.edu/SB2010/2010.09.10_mmff94x_ligs.tar.gz MMFF94x Ligands]
 
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Starting geometries optimized with gaff, opls, am1 and pm3mm were generated as well. These are available on request.
 
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== Copyright ==
 
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This database is derived from structures originally downloaded from the Protein Data Bank. This resource is meant to be freely useable by the docking community, both academic and commercial institutions. The manuscript for this work has been accepted and is currently in press.
 
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== Contact Information ==
 
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Please contact [[Image:Sudipto.email.png]] if you face any problems. <BR>
 
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Please report any structural errors or suggested protonation state improvements. We will incorporate them in future releases.
 

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"