# Difference between revisions of "SB2021.v1"

(13 intermediate revisions by the same user not shown) | |||

Line 2: | Line 2: | ||

== SB2021 Docking Database [2021.11.19 Initial Release]== | == SB2021 Docking Database [2021.11.19 Initial Release]== | ||

− | SB2021 is an updated release of the SB2012 docking validation database. | + | SB2021 is an updated release of the SB2012 docking validation database. The database has been updated to contain 1,172 protein-ligand complexes including addition protein structures bound to approved drug molecules, and new/ expanded sets of crossdocking families. Additionally 5 systems formerly in SB2012 have been removed as they did not align with the high quality standards of the set. Please refer to the publication [http://pubs.acs.org/doi/abs/10.1021/ci1001982 "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments"] for information regarding structure preparation. 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. |

Line 13: | Line 13: | ||

|- | |- | ||

| Receptors, Ligands and Spheres | | Receptors, Ligands and Spheres | ||

− | || [http://ringo.ams.sunysb.edu/downloads/ | + | || [http://ringo.ams.sunysb.edu/downloads/SB2021/2021_11_19.lig_rec_sph.tar.gz 2021_11_19.lig_rec_sph.tar.gz] |

|- | |- | ||

| Energy and Bump Grids | | Energy and Bump Grids | ||

− | || [http://ringo.ams.sunysb.edu/downloads/ | + | || [http://ringo.ams.sunysb.edu/downloads/SB2021/2021_11_19.grid_files.tar.gz 2021_11_19.grid_files.tar.gz] |

|- | |- | ||

− | | List of all systems (N = 1, | + | | List of all systems (N = 1,172) |

− | || [http://ringo.ams.sunysb.edu/downloads/ | + | || [http://ringo.ams.sunysb.edu/downloads/SB2021/clean.systems.all clean.systems.all] |

|} | |} | ||

+ | |||

+ | == SB2021 Protein Families == | ||

+ | |||

+ | Here are text files of systems in the database broken up by protein target. | ||

+ | (Only targets with <=8 structures are shown.) | ||

+ | |||

+ | {| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:60%" | ||

+ | |- style="background:lightblue" | ||

+ | ! style="width:100%" !|Resource | ||

+ | |||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/ABL_Kinase.txt ABL_Kinase] N= 24 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Acetylcholinesterase.txt Acetylcholinesterase] N= 20 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Adenosine_Deaminase.txt Adenosine_Deaminase] N= 8 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Beta_Trypsin.txt Beta_Trypsin] N= 29 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Carbonic_Anhydrase.txt Carbonic_Anhydrase] N= 31 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Carboxypeptidase_A.txt Carboxypeptidase_A] N= 8 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/CDK.txt CDK] N= 10 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Coagulation_Factor_Xa.txt Coagulation_Factor_Xa] N= 43 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/COX.txt COX] N= 9 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/EGFR.txt EGFR] N= 15 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Estrogen_Receptor.txt Estrogen_Receptor] N= 47 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/HIV_Protease.txt HIV_Protease] N= 66 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/HIV_Reverse_Transcriptase.txt HIV_Reverse_Transcriptase] N= 27 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/HMG_CoA_Reductase.txt HMG_CoA_Reductase] N= 19 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Hsp_90.txt Hsp_90] N= 13 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/IGF1_R.txt IGF1_R] N= 9 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/LpxC.txt LpxC] N= 33 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Lysozyme.txt Lysozyme] N= 14 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/MMP.txt MMP] N= 16 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Neuraminidase.txt Neuraminidase] N= 44 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Phosphodiesterase.txt Phosphodiesterase] N= 17 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/PPAR_Kinase.txt PPAR_Kinase] N= 21 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Protein_Tyrosine_Phosphatase.txt Protein_Tyrosine_Phosphatase] N= 20 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Ribonuclease_A.txt Ribonuclease_A] N= 14 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Streptavidin.txt Streptavidin] N= 8 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/T4_Lysozyme.txt T4_Lysozyme] N= 13 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Thermolysin.txt Thermolysin] N= 26 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Thrombin.txt Thrombin] N= 40 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Thymidylate_Synthase.txt Thymidylate_Synthase] N= 14 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Trypsin.txt Trypsin] N= 46 | ||

+ | |- | ||

+ | | [http://ringo.ams.sunysb.edu/downloads/SB2021/zzz.Family_Information/Vitamin_D_Nuclear_Receptor.txt Vitamin_D_Nuclear_Receptor] N= 38 |

## Latest revision as of 01:22, 19 November 2021

For more Rizzo Lab downloads: Rizzo Lab Downloads

## SB2021 Docking Database [2021.11.19 Initial Release]

SB2021 is an updated release of the SB2012 docking validation database. The database has been updated to contain 1,172 protein-ligand complexes including addition protein structures bound to approved drug molecules, and new/ expanded sets of crossdocking families. Additionally 5 systems formerly in SB2012 have been removed as they did not align with the high quality standards of the set. Please refer to the publication "Docking Validation Resources: Protein Family and Ligand Flexibility Experiments" for information regarding structure preparation. 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.

SB2021 is an on-going project.

Resource | Filename |
---|---|

Receptors, Ligands and Spheres | 2021_11_19.lig_rec_sph.tar.gz |

Energy and Bump Grids | 2021_11_19.grid_files.tar.gz |

List of all systems (N = 1,172) | clean.systems.all |

## SB2021 Protein Families

Here are text files of systems in the database broken up by protein target. (Only targets with <=8 structures are shown.)

Resource |
---|

ABL_Kinase N= 24 |

Acetylcholinesterase N= 20 |

Adenosine_Deaminase N= 8 |

Beta_Trypsin N= 29 |

Carbonic_Anhydrase N= 31 |

Carboxypeptidase_A N= 8 |

CDK N= 10 |

Coagulation_Factor_Xa N= 43 |

COX N= 9 |

EGFR N= 15 |

Estrogen_Receptor N= 47 |

HIV_Protease N= 66 |

HIV_Reverse_Transcriptase N= 27 |

HMG_CoA_Reductase N= 19 |

Hsp_90 N= 13 |

IGF1_R N= 9 |

LpxC N= 33 |

Lysozyme N= 14 |

MMP N= 16 |

Neuraminidase N= 44 |

Phosphodiesterase N= 17 |

PPAR_Kinase N= 21 |

Protein_Tyrosine_Phosphatase N= 20 |

Ribonuclease_A N= 14 |

Streptavidin N= 8 |

T4_Lysozyme N= 13 |

Thermolysin N= 26 |

Thrombin N= 40 |

Thymidylate_Synthase N= 14 |

Trypsin N= 46 |

Vitamin_D_Nuclear_Receptor N= 38 |