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| − | == SB2010 Docking Database [2010.05.19 Initial Release]==
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| − | 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.
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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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| − | 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. The Unbiased Ligand Structures were arbitrarily translated and rotated from the binding, and minimized in the absence of the receptor.
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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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| − | {| 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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| − | | Flexible Docked Ensembles
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| − | || To be released
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| − | |-
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| − | | Best Flex Docked Poses
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| − | || To be released
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| − | |-
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| − | | Unbiased Ligand Structures
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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+] [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] ==
| + | *[[SB2012]] Docking Testset (Expanded version of SB2010, N=1043 systems) |
| | + | **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) --> |
| | + | <!--**Database of files required for pose reproduction and crossdocking.--> |
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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. Clash subset indicates a subset of each protein family where inter-molecular clashes exist, which could possibly be resolved with flexible receptor docking. Aligned Structures contain the receptor and ligand mol2 files aligned to the first receptor in each family. | + | For lab members: The path to upload downloadable files on the Ringo server is found at |
| − | | + | /export/home/Downloads_path.txt |
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| − | {| border="1" cellpadding="3" cellspacing="0" style="background:white; text-align:left; width:80%"
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| − | ! style="width:40%" !| Protein Family
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| − | ! style="width:10%" !| Size
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| − | ! style="width:25%" !| Clash Subset
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| − | ! style="width:25%" !| Aligned Structures
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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| − | | [http://george.ams.sunysb.edu/SB2010/families.large/THROMBIN Thrombin]
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| − | | 37
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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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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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| − | | To be released
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| − | | To be released
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| − | |}
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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 useably by the docking community, both academic and commercial institutions. The manuscript for this work has been submitted and is currently under review.
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| − | == Contact Information ==
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| − | Please contact [[Image:Sudipto.email.png]] if you face any problems.
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