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aschreyer/fuzcav-calpha.sql

Created June 1, 2011 12:16
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Binding site similarity search in CREDO using the FuzCav algorithm
Raw
fuzcav-calpha.sql
SELECT s.pdb, l.ligand_name, s.title, sq.similarity
FROM (
WITH query AS (SELECT calphafp FROM credo.ligand_fuzcav WHERE ligand_id = 3919)
SELECT f.ligand_id, arrayxi_fuzcavsim_global(query.calphafp, f.calphafp) AS similarity
FROM credo.ligand_fuzcav f, query
WHERE arrayxi_fuzcavsim_global(query.calphafp, f.calphafp) > 0.17
) sq,
credo.ligands l, credo.biomolecules b, credo.structures s
WHERE sq.ligand_id = l.ligand_id
AND l.biomolecule_id = b.biomolecule_id
AND b.structure_id = s.structure_id
ORDER BY 4 DESC;
pdb | ligand_name | title | similarity
------+-------------+-----------------------------------------------------------------------------------------+-------------------
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 1
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.609710550887022
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.548094373865699
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.482511210762332
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.454722492697176
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.408834586466165
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.312681510164569
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.3047711781889
2GQG | 1N1 | X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain | 0.283349561830574
2GQG | 1N1 | X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain | 0.251792114695341
3G0F | B49 | KIT kinase domain mutant D816H in complex with sunitinib | 0.23141186299081
3G0F | B49 | KIT kinase domain mutant D816H in complex with sunitinib | 0.23141186299081
1T46 | STI | STRUCTURAL BASIS FOR THE AUTOINHIBITION AND STI-571 INHIBITION OF C-KIT TYROSINE KINASE | 0.227903579254931
1UWH | BAX | THE COMPLEX OF WILD TYPE B-RAF AND BAY439006 | 0.215167548500882
1UWH | BAX | THE COMPLEX OF WILD TYPE B-RAF AND BAY439006 | 0.211775043936731
3G0F | B49 | KIT kinase domain mutant D816H in complex with sunitinib | 0.206185567010309
3G0F | B49 | KIT kinase domain mutant D816H in complex with sunitinib | 0.206185567010309
1UWJ | BAX | THE COMPLEX OF MUTANT V599E B-RAF AND BAY439006 | 0.197718631178707
3G0E | B49 | KIT kinase domain in complex with sunitinib | 0.195280716029292
1UWJ | BAX | THE COMPLEX OF MUTANT V599E B-RAF AND BAY439006 | 0.183212267958031
1KV2 | B96 | Human p38 MAP Kinase in Complex with BIRB 796 | 0.17332035053554
2XKD | T3M | STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12 | 0.171735241502683
(22 rows)
Raw
fuzcav-rep.sql
SELECT s.pdb, l.ligand_name, s.title, sq.similarity
FROM (
WITH query AS (SELECT repfp FROM credo.ligand_fuzcav WHERE ligand_id = 3919)
SELECT f.ligand_id, arrayxi_fuzcavsim_global(query.repfp, f.repfp) AS similarity
FROM credo.ligand_fuzcav f, query
WHERE arrayxi_fuzcavsim_global(query.repfp, f.repfp) > 0.13
) sq,
credo.ligands l, credo.biomolecules b, credo.structures s
WHERE sq.ligand_id = l.ligand_id
AND l.biomolecule_id = b.biomolecule_id
AND b.structure_id = s.structure_id
ORDER BY 4 DESC;
pdb | ligand_name | title | similarity
------+-------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 1
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.56701030927835
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.441840277777778
2HYY | STI | Human Abl kinase domain in complex with imatinib (STI571, Glivec) | 0.412064570943076
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.336538461538462
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.326495726495727
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.308191403081914
3CS9 | NIL | Human ABL kinase in complex with nilotinib | 0.286181520850368
1UWJ | BAX | THE COMPLEX OF MUTANT V599E B-RAF AND BAY439006 | 0.169976171564734
2GQG | 1N1 | X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain | 0.169971671388102
2GQG | 1N1 | X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain | 0.165250236071766
1UWH | BAX | THE COMPLEX OF WILD TYPE B-RAF AND BAY439006 | 0.1608
1UWH | BAX | THE COMPLEX OF WILD TYPE B-RAF AND BAY439006 | 0.160354552780016
1T46 | STI | STRUCTURAL BASIS FOR THE AUTOINHIBITION AND STI-571 INHIBITION OF C-KIT TYROSINE KINASE | 0.152096659559346
2XKD | T3M | STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12 | 0.14577530176416
1JZ3 | BTB | E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE | 0.143531633616619
1JZ3 | BTB | E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE | 0.143531633616619
2ONM | ADP | Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+ | 0.136921624173749
2ONM | ADP | Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+ | 0.136921624173749
1F5L | AMR | UROKINASE PLASMINOGEN ACTIVATOR B-CHAIN-AMILORIDE COMPLEX | 0.135234590616375
1UWJ | BAX | THE COMPLEX OF MUTANT V599E B-RAF AND BAY439006 | 0.134588563458856
1S9P | DES | crystal structure of the ligand-binding domain of the estrogen-related receptor gamma in complex with diethylstilbestrol | 0.134088762983947
2JF9 | OHT | ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC PEPTIDE ANTAGONIST | 0.134088762983947
2JF9 | OHT | ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC PEPTIDE ANTAGONIST | 0.134088762983947
1U72 | MTX | Understanding the Role of Leu22 Variants in Methotrexate Resistance: Comparison of Wild-type and Leu22Arg Variant Mouse and Human Dihydrfolate Reducta | 0.133628318584071
1S9P | DES | crystal structure of the ligand-binding domain of the estrogen-related receptor gamma in complex with diethylstilbestrol | 0.13314447592068
2ONM | ADP | Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with NAD+ | 0.132200188857413
3N1T | 5GP | Crystal structure of the H101A mutant ecHint GMP complex | 0.13023610053313
3NXU | RIT | Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir | 0.130094043887147
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