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Ligand pose and orientational sampling in molecular docking.
(2013) PLoS One 8
PubMed: 24098414 | PubMedCentral: PMC3787967 | DOI: 10.1371/journal.pone.0075992
For 13 PDB  structures of Glutamate receptor ionotropic kainate 1 (GRIK1) (1VSO, 2F34, 2F35, 2PBW, 2QS1, 2QS2, 2QS3, 2WKY, 3C31, 3GBA, 3GBB, 3S2V, 4DLD), the ligands were extracted and compared to... their docked poses based on the heavy atom root mean square deviation (RMSD) using the Kuhn–Munkres algorithm  to account for symmetry.
Publication Year: 2013
PubMed ID is not available.
Published in 2014
Table 1 Targets for SPLIF Benchmarking Collected from DUD-E class target description PDB actives a decoys a Gscore cutoff b refs kinase FAK1 focal adhesion kinase 1 3bz3 100 (71) 5350 ... 2131) –6.0 ( 9 ) (1mp8, 2etm, 2ijm, 3bz3, 4gu6, 4gu9, 4i4e, 4k8a, 4kab) AKT1 serine/threonine-protein kinase AKT 3cqw 293 (199) 16450 (6131) –5.0 ( 12 ) (3cqu, 3cqw, 3mv5, 3mvh, 3ocb, 3ow4, 3qkk, 3cql, 3qkm, 4ekk, 4ekl, 4gv1) protease ACE angiotensin-converting enzyme 3bkl 282 (277) 16900 (16454) –2.5 ( 13 ) (1o86, 1uze, 1uzf, 2c6n, 2oc2, 2xy9, 2xyd, 2ydm, 3bkk, 3bkl, 3l3n, 3nxq, 4bxk) TRYB1 tryptase beta-1 2zec 148 (59) 7650 (1657) –6.0 ( 5 ) (2f9p, 2f9n, 2zeb, 2zec, 4a6l) HMDH HMG-CoA reductase 3ccw 170 (170) 8750 (8456) –2.5 22 (1dq8, 1dq9, 1dqa, 1hw8, 1hw9, 1hwi, 1hwj, 1hwk, 1hwl, 2q1l, 2q6b, 2q6c, 2r4f, 3bgl, 3cct, 3ccw, 3ccz, 3cd0, 3cd5, 3cd7, 3cda, 3cdb) GPCR ADRB1 Beta-1 adrenergic receptor 2vt4 247 (240) 15842 (13932) –4.0 ( 14 ) (2vt4, 2y00, 2y01, 2y02, 2y03, 2y04, 2ycw, 2ycx, 2ycy, 2ycz, 3zpq, 3zpr, 4ami, 4amj) nuclear receptor MCR mineralocorticoid receptor 2aa2 94 (66) 5150 (2481) –6.0 ( 13 ) (2aa2, 1y9r, 1ya3, 2a3i, 2aa5, 2aa6, 2aa7, 2aax, 2ab2, 2abi, 2oax, 3vhu, 3vhv) PRGR progesterone receptor 3kba 293 (222) 15650 (12914) –5.0 ( 17 ) (1a28, 1e3k, 1sqn, 1sr7, 1zuc, 2ovh, 2ovm, 2w8y, 3d90, 3g8o, 3hq5, 3kba, 3zr7, 3zra, 3zrb, 4a2j, 4apu) ion channel GRIK1 glutamate receptor ionotropic kainate 1 1vso 101 (96) 6550 (5980) –2.5 ( 17 ) (1txf, 1vso, 1ycj, 2f34, 2f35, 2f36, 2pbw, 2qs1, 2qs2, 2qs3, 2qs4, 2wky, 3gba, 3gbb, 3s2v, 4dld, 4e0x) synthase PGH2 cyclooxygenase-2 3ln1 435 (374) 23150 (17948) –5.0 27 (1cvu, 1cx2, 1ddx, 1pxx, 3hs5, 3hs6, 3hs7, 3krk, 3ln0, 3ln1, 3mdl, 3nt1, 3ntb, 3ntg, 3olt, 3olu, 3pgh, 3q7d, 3qh0, 3qmq, 3rr3, 3tzi, 4cox, 4e1g, 4fm5, 4llz, 6cox) a Initial numbers of actives and decoys from DUD-E with the numbers after the Gscore filter included in parentheses.
Publication Year: 2014
Synthesis and molecular docking of novel non-competitive antagonists of GluK2 receptor.
Med Chem Res 24
PubMed: 25620864 | PubMedCentral: PMC4295030 | DOI: 10.1007/s00044-014-1171-1
, 2011 ) and the ligand-binding domain (crystal structure of GluK1 ligand-binding domain (S1S2) in complex with an antagonist, PDB ID: 4DLD) (Venskutonytė et al .
Publication Year: null
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