GPCR-Bench provides a high quality GPCR docking benchmarking set: 25 PDB structures covering all NR structures as of January 2015, and active and decoy compounds in the spirit of DUD.
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5HT1B.fxx Files for the GPCR-Bench set Oct 12, 2015
5HT1B.mol2 Files for the GPCR-Bench set Oct 12, 2015
5HT1B.pdb Files for the GPCR-Bench set Oct 12, 2015
5HT1B.zip Files for the GPCR-Bench set Oct 12, 2015
5HT1B_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
5HT1B_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
5HT1B_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
5HT1B_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
5HT2B.fxx Files for the GPCR-Bench set Oct 12, 2015
5HT2B.mol2 Files for the GPCR-Bench set Oct 12, 2015
5HT2B.pdb Files for the GPCR-Bench set Oct 12, 2015
5HT2B.zip Files for the GPCR-Bench set Oct 12, 2015
5HT2B_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
5HT2B_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
5HT2B_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
5HT2B_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
AA2AR.fxx Files for the GPCR-Bench set Oct 12, 2015
AA2AR.mol2 Files for the GPCR-Bench set Oct 12, 2015
AA2AR.pdb Files for the GPCR-Bench set Oct 12, 2015
AA2AR.zip Files for the GPCR-Bench set Oct 12, 2015
AA2AR_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
AA2AR_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
AA2AR_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
AA2AR_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
ACM2.fxx Files for the GPCR-Bench set Oct 12, 2015
ACM2.mol2 Files for the GPCR-Bench set Oct 12, 2015
ACM2.pdb Files for the GPCR-Bench set Oct 12, 2015
ACM2.zip Files for the GPCR-Bench set Oct 12, 2015
ACM2_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
ACM2_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
ACM2_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
ACM2_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
ACM3.fxx Files for the GPCR-Bench set Oct 12, 2015
ACM3.mol2 Files for the GPCR-Bench set Oct 12, 2015
ACM3.pdb Files for the GPCR-Bench set Oct 12, 2015
ACM3.zip Files for the GPCR-Bench set Oct 12, 2015
ACM3_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
ACM3_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
ACM3_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
ACM3_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
ADRB1.fxx Files for the GPCR-Bench set Oct 12, 2015
ADRB1.mol2 Files for the GPCR-Bench set Oct 12, 2015
ADRB1.pdb Files for the GPCR-Bench set Oct 12, 2015
ADRB1.zip Files for the GPCR-Bench set Oct 12, 2015
ADRB1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
ADRB1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
ADRB1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
ADRB1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
ADRB2.fxx Files for the GPCR-Bench set Oct 12, 2015
ADRB2.mol2 Files for the GPCR-Bench set Oct 12, 2015
ADRB2.pdb Files for the GPCR-Bench set Oct 12, 2015
ADRB2.zip Files for the GPCR-Bench set Oct 12, 2015
ADRB2_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
ADRB2_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
ADRB2_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
ADRB2_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
B1AR.zip Files for the GPCR-Bench set Oct 12, 2015
CCR5.fxx Files for the GPCR-Bench set Oct 12, 2015
CCR5.mol2 Files for the GPCR-Bench set Oct 12, 2015
CCR5.pdb Files for the GPCR-Bench set Oct 12, 2015
CCR5.zip Files for the GPCR-Bench set Oct 12, 2015
CCR5_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
CCR5_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
CCR5_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
CCR5_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
CRFR1.fxx Files for the GPCR-Bench set Oct 12, 2015
CRFR1.mol2 Files for the GPCR-Bench set Oct 12, 2015
CRFR1.pdb Files for the GPCR-Bench set Oct 12, 2015
CRFR1.zip Files for the GPCR-Bench set Oct 12, 2015
CRFR1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
CRFR1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
CRFR1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
CRFR1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
CXCR4.fxx Files for the GPCR-Bench set Oct 12, 2015
CXCR4.mol2 Files for the GPCR-Bench set Oct 12, 2015
CXCR4.pdb Files for the GPCR-Bench set Oct 12, 2015
CXCR4.zip Files for the GPCR-Bench set Oct 12, 2015
CXCR4_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
CXCR4_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
CXCR4_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
CXCR4_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
DRD3.fxx Files for the GPCR-Bench set Oct 12, 2015
DRD3.mol2 Files for the GPCR-Bench set Oct 12, 2015
DRD3.pdb Files for the GPCR-Bench set Oct 12, 2015
DRD3.zip Files for the GPCR-Bench set Oct 12, 2015
DRD3_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
DRD3_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
DRD3_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
DRD3_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
GPR40.fxx Files for the GPCR-Bench set Oct 12, 2015
GPR40.mol2 Files for the GPCR-Bench set Oct 12, 2015
GPR40.pdb Files for the GPCR-Bench set Oct 12, 2015
GPR40.zip Files for the GPCR-Bench set Oct 12, 2015
GPR40_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
GPR40_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
GPR40_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
GPR40_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
HRH1.fxx Files for the GPCR-Bench set Oct 12, 2015
HRH1.mol2 Files for the GPCR-Bench set Oct 12, 2015
HRH1.pdb Files for the GPCR-Bench set Oct 12, 2015
HRH1.zip Files for the GPCR-Bench set Oct 12, 2015
HRH1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
HRH1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
HRH1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
HRH1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
MGLUR1.fxx Files for the GPCR-Bench set Oct 12, 2015
MGLUR1.mol2 Files for the GPCR-Bench set Oct 12, 2015
MGLUR1.pdb Files for the GPCR-Bench set Oct 12, 2015
MGLUR1.zip Files for the GPCR-Bench set Oct 12, 2015
MGLUR1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
MGLUR1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
MGLUR1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
MGLUR1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
MGLUR5.mol2 Files for the GPCR-Bench set Oct 12, 2015
MGLUR5.pdb Files for the GPCR-Bench set Oct 12, 2015
MGLUR5.zip Files for the GPCR-Bench set Oct 12, 2015
MGLUR5_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
MGLUR5_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
MGLUR5_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
MGLUR5_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
MLGUR1.zip Files for the GPCR-Bench set Oct 12, 2015
OPRD.fxx Files for the GPCR-Bench set Oct 12, 2015
OPRD.mol2 Files for the GPCR-Bench set Oct 12, 2015
OPRD.pdb Files for the GPCR-Bench set Oct 12, 2015
OPRD.zip Files for the GPCR-Bench set Oct 12, 2015
OPRD_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
OPRD_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
OPRD_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
OPRD_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
OPRK.fxx Files for the GPCR-Bench set Oct 12, 2015
OPRK.mol2 Files for the GPCR-Bench set Oct 12, 2015
OPRK.pdb Files for the GPCR-Bench set Oct 12, 2015
OPRK.zip Files for the GPCR-Bench set Oct 12, 2015
OPRK_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
OPRK_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
OPRK_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
OPRK_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
OPRM.fxx Files for the GPCR-Bench set Oct 12, 2015
OPRM.mol2 Files for the GPCR-Bench set Oct 12, 2015
OPRM.pdb Files for the GPCR-Bench set Oct 12, 2015
OPRM.zip Files for the GPCR-Bench set Oct 12, 2015
OPRM_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
OPRM_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
OPRM_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
OPRM_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
OPRX.fxx Files for the GPCR-Bench set Oct 12, 2015
OPRX.mol2 Files for the GPCR-Bench set Oct 12, 2015
OPRX.pdb Files for the GPCR-Bench set Oct 12, 2015
OPRX.zip Files for the GPCR-Bench set Oct 12, 2015
OPRX_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
OPRX_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
OPRX_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
OPRX_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
OX2R.fxx Files for the GPCR-Bench set Oct 12, 2015
OX2R.mol2 Files for the GPCR-Bench set Oct 12, 2015
OX2R.pdb Files for the GPCR-Bench set Oct 12, 2015
OX2R.zip Files for the GPCR-Bench set Oct 12, 2015
OX2R_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
OX2R_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
OX2R_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
OX2R_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
P2Y12.fxx Files for the GPCR-Bench set Oct 12, 2015
P2Y12.mol2 Files for the GPCR-Bench set Oct 12, 2015
P2Y12.pdb Files for the GPCR-Bench set Oct 12, 2015
P2Y12.zip Files for the GPCR-Bench set Oct 12, 2015
P2Y12_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
P2Y12_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
P2Y12_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
P2Y12_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
PAR1.fxx Files for the GPCR-Bench set Oct 12, 2015
PAR1.mol2 Files for the GPCR-Bench set Oct 12, 2015
PAR1.pdb Files for the GPCR-Bench set Oct 12, 2015
PAR1.zip Files for the GPCR-Bench set Oct 12, 2015
PAR1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
PAR1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
PAR1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
PAR1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
README.md Create README.md Oct 12, 2015
S1PR1.fxx Files for the GPCR-Bench set Oct 12, 2015
S1PR1.mol2 Files for the GPCR-Bench set Oct 12, 2015
S1PR1.pdb Files for the GPCR-Bench set Oct 12, 2015
S1PR1.zip Files for the GPCR-Bench set Oct 12, 2015
S1PR1_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
S1PR1_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
S1PR1_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
S1PR1_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
SMO.fxx Files for the GPCR-Bench set Oct 12, 2015
SMO.mol2 Files for the GPCR-Bench set Oct 12, 2015
SMO.pdb Files for the GPCR-Bench set Oct 12, 2015
SMO.zip Files for the GPCR-Bench set Oct 12, 2015
SMO_chembl19_set.sdf.bz2 Files for the GPCR-Bench set Oct 12, 2015
SMO_chembl19_set.smi Files for the GPCR-Bench set Oct 12, 2015
SMO_diverse_actives.id Files for the GPCR-Bench set Oct 12, 2015
SMO_dude_decoys.id Files for the GPCR-Bench set Oct 12, 2015
oldADRB1.zip Files for the GPCR-Bench set Oct 12, 2015

README.md

GPCR-Bench

GPCR-Bench provides a high quality GPCR docking benchmarking set: 25 PDB structures covering all NR structures as of January 2015, and active and decoy compounds in the spirit of DUD.

How to use

Download files for your GPCR target of choice, or download all to run a comparison of methods for all 25 GPCR targets.

File descriptions

  • Receptor_chembl19_set.sdf.bz2

3D coordinates for all the molecules in the benchmarking set (~200 actives and ~10000 decoys). Ligands were prepared with the software MoKa and CORINA. The tautomeric states with a minimum abundance threshold of 20% were generated with TAUTHOR and the ionic states with a minimum abundance threshold of 10% at pH 7.4 with BLABBER. All low energy 3D conformations were created with CORINA including up-to 10 ring conformations per molecule in an energy window of ~2 kcal/mol.

  • Receptor_chembl19_set.smi

Smiles strings of all the molecules in the benchmarking set (~200 actives and ~10000 decoys).

  • Receptor_diverse_actives.id

ID names of all the actives in the set.

  • Receptor_dude_decoys.id

ID names of all the decoys in the set.

  • Receptor.pdb

Clean PDB file of the high resolution crystal structure containing only the protein coordinates.

  • Receptor.mol2

MOL2 structure file of the co-crystal ligand with hydrogens included

  • Receptor.zip

MAESTRO grid zip file for GLIDE (Schrodinger) docking

  • Receptor.fxx

HYDE (Biosolveit) receptor file

Ligand Retrieval from ChEMBL19.

Ligands were extracted for each target from the ChEMBL19 database, using an automated script based on the ChEMBL Web Service API. Only compounds with bioactivity_type corresponding to Ki, Kd, IC50 or EC50 and with a value less than or equal to 10000 were stored. Compounds with assay_description matching PUBCHEM_BIOASSAY or DRUGMATRIX were not included as these data sources led to many false positives in the set. Compounds were then filtered for 'drug-likeness', which included the following terms: Sulfur Count <=2; Chlorine Count <=3 ; Bromine Count <=1 ; Iodine Count <=1; Fluorine Count <=6; 250 <= Molecular Weight <= 500 ; 0 <= H-Donors <= 4 ; 1 <= H-Acceptors <= 8; 0 <= Rotatable Bonds <=7; Rings <= 5; # of Atoms >= 12. Targets for which there were still over 1000 ligands were further filtered to include only Ki values, and only ligands with Ki <= 100nM; Targets with over 400 ligands included Ki, Kd, IC50 or EC50 with value <= 100nM; all other targets had less than 400 ligands and included Ki, Kd, IC50 or EC50 with value <= 10000nM. Finally, for all targets with more than 200 ligands, 200 maximally diverse ligands were chosen using the 'Diverse Molecules' component in PipelinePilot9.1 based on ECFP4 fingerprints. To each set we also added all the co-crystal ligands available in the PDB, which is important for cross docking experiments.

Decoy generation.

http://dude.docking.org/

Mysinger MM, Carchia M, Irwin JJ, Shoichet BK J. Med. Chem., 2012, Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking