Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines
Montiago X. LaBute, Xiaohua Zhang, Jason Lenderman, Brian Bennion, Sergio E. Wong, Felice C. Lightstone
PLoS ONE (2014) 9(9): e106298.

Docking scores - 560 ligands (drugs) vs. 409 targets (proteins)

N560_p409_DockScore_Matrix.csv

DrugBank interaction indicators - 560 drugs vs. 555 proteins (on-target proteins)

N560_p555_DB_Matrix.csv

Raw MMGB/SA re-scored docking scores - 560 drugs vs. 33 proteins (virtual toxicity panel)

N560_p33_MMGBSAScore_Matrix.csv

DrugBank interaction indicators - 560 drugs vs. 16 proteins (virtual toxicity panel - on-target proteins)

N560_p16_DB_Matrix.csv

UniProt-to-PDB mapping for virtual toxicity panel (Excel file)

VirtualToxPanel_UniProtToPDB_Mapping.xlsx

Interaction indicators - 560 drugs vs. adverse drug reaction phenotype groups collected from SIDER

N560_p10_DrugADR_Matrix.csv

R scripts

README.txt - Descriptions of each script, including inputs, outputs, and R package dependencies.

TenFoldCVTimesTen_VinaLC.R
TenFoldCVTimesTen_DrugBank.R
TenFoldCVTimesTen_VirtualToxicityPanel_MMGBSA.R
TenFoldCVTimesTen_VirtualToxicityPanel_DrugBank.R
CalcPValue_Example.R

Top-ranked poses by target protein

1ald 1bg2 1bj4 1bx4 1byw 1cza 1d1j 1d1t 1dkt 1dok 1edm 1eqt 1ext 1f6w 1fcy 1fgk 1fil 1fmk 1fw1 1fyh 1g3m 1gen 1gpl 1gs9 1h03 1h45 1h6i 1h9u 1hdo 1hdr 1hfc 1hnf 1hul 1hup 1hur 1i0z 1i3m 1i71 1i8l 1ijq 1ijt 1ikt 1ipb 1j99 1jbq 1jcn 1jdw 1jj7 1jk7 1jl9 1jlj 1jtv 1khb 1khx 1kqn 1lf7 1lj5 1ls6 1lv2 1m13 1m48 1m9d 1m9m 1m9z 1meo 1mh1 1mjn 1mlw 1mp8 1mq0 1mso 1n3l 1n46 1n83 1nb0 1ncn 1nf7 1nm8 1nn5 1nn6 1nnl 1now 1nrg 1nu4 1nuu 1o6l 1o7z 1ogw 1ohq 1osh 1oth 1p49 1p5z 1pfq 1pkx 1pq3 1pq9 1pv8 1q0p 1q20 1qcf 1qnt 1qqd 1r3s 1r6u 1r9o 1rlw 1ryo 1siq 1smo 1so7 1sqn 1taz 1tev 1u3t 1u3u 1u3w 1u59 1ua2 1ucn 1uj2 1umk 1uou 1uuh 1uw5 1vca 1vec 1w4r 1w6k 1wlj 1wrk 1wwb 1www 1x88 1x8b 1x9d 1x9n 1xap 1xbb 1xjd 1xtq 1xw6 1y2k 1yow 1yrk 1z4r 1z6z 1z8d 1zjk 1zkl 1zn8 1zs9 2a1x 2a2r 2aeb 2ag4 2arr 2ax6 2aze 2b50 2b5g 2bh9 2ble 2br9 2btz 2bzg 2c47 2c95 2c9y 2cbz 2cm2 2coi 2cw6 2ddf 2dho 2dko 2e0a 2e2r 2e8a 2esk 2f15 2f8a 2fcb 2fdv 2fh1 2fmp 2fvl 2fy7 2g76 2gk2 2gl8 2gys 2h5g 2h63 2heh 2hft 2hgs 2hi4 2i0e 2ib8 2ic1 2iip 2iuw 2izz 2jak 2jis 2jk2 2jkv 2mcg 2ngr 2nnj 2nru 2nvh 2nz2 2o3h 2o4j 2oat 2obv 2okj 2okk 2om2 2oo0 2oq1 2our 2ozl 2p26 2pez 2pid 2q32 2q8g 2qis 2ql9 2qqi 2qyk 2qym 2r2n 2r3i 2r3v 2rep 2rhi 2v40 2v7o 2vif 2vn9 2vo1 2vpi 2vx3 2vz6 2w3l 2w4o 2w8n 2w96 2wcb 2wgh 2wsl 2wy8 2wzb 2x25 2xfn 2xsn 2y7l 2yk9 2yl2 2yx8 2yxt 2z5y 2z62 2z7r 2z80 2znn 2zoq 2zt5 3a4o 3a4u 3agm 3ara 3b2t 3b6h 3b6r 3b6u 3b7o 3bg8 3bgs 3bhh 3bj5 3bl9 3bpt 3buv 3bzi 3c6k 3cb2 3cbb 3cbp 3cc6 3cmq 3cog 3crk 3czd 3d44 3dhf 3dhp 3dmw 3dyd 3dyn 3e7a 3e7o 3eaz 3ecm 3ed7 3eml 3eqc 3eqm 3esk 3euf 3ewy 3f9m 3fdl 3fdn 3fhr 3fvk 3fvs 3gft 3gg3 3ggf 3glk 3glr 3h8r 3h9e 3hf1 3hg3 3hl5 3hmi 3hmm 3hms 3hqa 3i4w 3ibd 3ihj 3ii0 3ij8 3ik7 3inm 3isq 3itu 3iw4 3k22 3k6p 3kfd 3ks9 3ld6 3ldo 3lmk 3lpp 3ls8 3max 3mjh 3mtc 3n7s 3nsz 3o2g 3o8y 3olj 3orh 3osk 3ovx 3oy1 3p23 3pa3 3pcv 3qxm 3s8w 3s98 3sm9 3u10 3zrk 4gtu 5hpg 2fm0 2r4r 2r4s 2rh1 2ydo 2ydv 2z5x 3d4s 3kk6 3nt1 3ny8 3ny9 3nya 3p0g 3pds 3pwh 3qak 3rey 3rfm 3rze 3sn6 3uon 3uza 3uzc 3v49 4daj 4djh 4dkl 4ej4 4gbr 4iaq 4iar

Download top docking poses, all targets and ligands

plosone-t409-1560.tar.gz (1.4 GB)

LLNL-WEB-655656