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Full 300-drug HDAC2 screen: specificity achieved, BG-1003 top hit

Browse Source 
Corrected pipeline ran clean: 1 MSA query, 299/299 screened, 0 failures,
~$5-8 (vs the fragile 2.5hr/$15 version).

Results:
- Scale validation: HDAC inhibitors rank 1-9 (>=0.99); valproic-acid 0.90.
- DECISIVE specificity: best negative control = cetirizine rank 44 (P=0.39);
  all 26 negative controls rank low. Co-folding REJECTS unrelated drugs --
  exactly what connectivity could not do (where norethindrone/ciprofloxacin
  ranked top). The modality-pivot thesis vindicated at screen scale.
- Discovery: BG-1003 (rank 5, P=0.997, random sample) is the standout
  non-obvious binder, above several known HDAC inhibitors; also JW55,
  BRD-K14666757. 11 drugs P>0.9 (8 known inhibitors + 3 non-obvious).

Caveats kept honest: BG-1003 may be a known HDAC inhibitor in the random
sample (validation, not novelty) -- needs identity check; binding != efficacy;
prodrug/macrocycle false negatives. Full ranking in docs/results/.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
Junior B.
2026-06-26 10:05:06 +02:00
parent 98c99bc271
commit 71069d3f10
2 changed files with 328 additions and 1 deletions
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rank,drug,P_binder,affinity,inclusion_reason
1,trichostatin-a,0.9995425343513489,-2.8145930767059326,related_mechanism
2,vorinostat,0.9994102716445923,-1.736063003540039,related_mechanism
3,panobinostat,0.9985321760177612,-2.5815885066986084,related_mechanism
4,belinostat,0.9969940185546875,-2.1257152557373047,related_mechanism
5,BG-1003,0.9969587326049805,-1.7902384996414185,general_sample
6,scriptaid,0.9953755140304565,-1.604792833328247,related_mechanism
7,mocetinostat,0.9910330772399902,-1.1003236770629883,related_mechanism
8,entinostat,0.9900848865509033,-0.66916424036026,related_mechanism
9,apicidin,0.9881076812744141,-2.1283297538757324,related_mechanism
10,BRD-K14666757,0.9683372974395752,-0.6549662351608276,general_sample
11,JW55,0.9362592697143555,-0.4662295877933502,general_sample
12,valproic-acid,0.8981399536132812,0.37430477142333984,related_mechanism
13,FIT,0.8313940763473511,0.08768215775489807,general_sample
14,hydroxyurea,0.7578531503677368,1.246307611465454,ground_truth
15,ibuprofen,0.7412509918212891,2.238396167755127,related_mechanism
16,sulforaphane,0.739348292350769,0.3284870982170105,related_mechanism
17,BRD-K10302728,0.7058488130569458,-0.9450978636741638,general_sample
18,BRD-K61285042,0.6548928022384644,0.49822238087654114,general_sample
19,ciprofibrate,0.633934736251831,1.9368321895599365,general_sample
20,KI-16425,0.6012023091316223,0.6640514731407166,general_sample
21,curcumin,0.5989675521850586,1.486403226852417,related_mechanism
22,BRD-K29660619,0.5905249118804932,0.12171633541584015,general_sample
23,resveratrol,0.5783771276473999,1.2722764015197754,related_mechanism
24,BRD-K27824357,0.564523458480835,0.1906198263168335,general_sample
25,tadalafil,0.5615900754928589,0.007123969495296478,related_mechanism
26,BRD-K46241566,0.5496933460235596,0.8938988447189331,general_sample
27,BRD-K99633092,0.5473401546478271,-0.44378313422203064,general_sample
28,BRD-K32389477,0.5432510375976562,-0.9505497813224792,general_sample
29,talnetant,0.5365580320358276,-0.4235907196998596,general_sample
30,montelukast,0.5170086622238159,0.7837215662002563,related_mechanism
31,tetracaine,0.514898419380188,0.486468642950058,general_sample
32,SA-1480001,0.5129876732826233,-0.14114731550216675,general_sample
33,lawsone,0.5126880407333374,1.3275636434555054,general_sample
34,quercetin,0.5112301111221313,0.35112306475639343,related_mechanism
35,BRD-K67328514,0.47897130250930786,1.6453043222427368,general_sample
36,glutamine,0.4580795168876648,2.2292144298553467,ground_truth
37,romidepsin,0.438159316778183,-0.6780526638031006,related_mechanism
38,BRD-K19362120,0.43379056453704834,-0.38182151317596436,general_sample
39,rifaximin,0.43118005990982056,-0.007878035306930542,general_sample
40,palmitoylethanolamide,0.4253748655319214,1.5332996845245361,general_sample
41,D-64131,0.4243965148925781,1.8345916271209717,general_sample
42,deferasirox,0.414570152759552,0.8550795912742615,related_mechanism
43,BRD-K39379309,0.39516061544418335,1.2569950819015503,general_sample
44,cetirizine,0.39126813411712646,1.497683048248291,negative_control
45,decitabine,0.3905729651451111,0.9013112783432007,related_mechanism
46,ingenol,0.38832157850265503,1.2636841535568237,general_sample
47,BRD-K02558072,0.38382846117019653,1.3527982234954834,general_sample
48,lestaurtinib,0.37580811977386475,0.5706255435943604,general_sample
49,BRD-K22546959,0.373577356338501,1.4228181838989258,general_sample
50,sulfasalazine,0.3713478446006775,0.9489234089851379,related_mechanism
51,brompheniramine,0.36528241634368896,0.7533001899719238,general_sample
52,SKI-II,0.3633918762207031,1.0488131046295166,general_sample
53,BRD-K03142004,0.3538649380207062,0.4557762145996094,general_sample
54,miltefosine,0.3524576723575592,1.3234755992889404,general_sample
55,lidocaine,0.3505249321460724,2.832113265991211,negative_control
56,omeprazole,0.3403707444667816,1.4137210845947266,negative_control
57,BW-B70C,0.34008413553237915,1.2555820941925049,general_sample
58,azacitidine,0.33303695917129517,0.8310854434967041,related_mechanism
59,KO-143,0.33238181471824646,-0.9562602043151855,general_sample
60,trioxsalen,0.33212581276893616,2.046276569366455,general_sample
61,dexchlorpheniramine,0.3283562660217285,1.02620530128479,general_sample
62,ciprofloxacin,0.32668250799179077,0.26640501618385315,negative_control
63,aspirin,0.3254982829093933,2.339493751525879,related_mechanism
64,BRD-K55966666,0.3211105465888977,-0.2134701907634735,general_sample
65,carisoprodol,0.3141220510005951,1.6034519672393799,general_sample
66,tetracycline,0.31255578994750977,1.2801803350448608,negative_control
67,atorvastatin,0.3122830092906952,0.5527983903884888,related_mechanism
68,BRD-K19105325,0.3045218586921692,-0.2390911877155304,general_sample
69,BRD-A27640568,0.3026970326900482,1.965691328048706,general_sample
70,phenolphthalein,0.3001948595046997,0.9219919443130493,general_sample
71,BRD-K71182391,0.29757264256477356,0.5220360159873962,general_sample
72,BRD-K38061943,0.2891416549682617,0.14858180284500122,general_sample
73,BRD-K93445052,0.28817978501319885,0.7619435787200928,general_sample
74,halofantrine,0.28806358575820923,0.008057385683059692,general_sample
75,BRD-K16912444,0.28658565878868103,-0.0714123547077179,general_sample
76,BRD-K39431601,0.2835044860839844,-0.3456823229789734,general_sample
77,LY-341495,0.27582740783691406,0.44341373443603516,general_sample
78,tyrphostin-A9,0.2754404842853546,1.5046072006225586,general_sample
79,BRD-K87449690,0.26641374826431274,2.289837121963501,general_sample
80,BRD-K87720600,0.2651839256286621,0.2896602153778076,general_sample
81,fexofenadine,0.26415905356407166,1.2466082572937012,negative_control
82,BRD-K33284065,0.2630389928817749,0.6950460076332092,general_sample
83,ITE,0.257363498210907,1.146105170249939,general_sample
84,amoxicillin,0.25568023324012756,1.8630526065826416,negative_control
85,BRD-K45889441,0.25448158383369446,0.6300027966499329,general_sample
86,BRD-K52524742,0.25103557109832764,1.058586835861206,general_sample
87,methotrexate,0.24424436688423157,1.9891445636749268,general_sample
88,BRD-K67470788,0.24184325337409973,1.50880765914917,general_sample
89,ethinyl-estradiol,0.24175500869750977,1.410076379776001,negative_control
90,lisinopril,0.2400914877653122,1.5881357192993164,general_sample
91,BRD-K93411257,0.23802407085895538,-0.2541484236717224,general_sample
92,BRD-K71353154,0.23799994587898254,0.5835225582122803,general_sample
93,cyclazosin,0.23158416152000427,0.03154781460762024,general_sample
94,BRD-K74271701,0.23076415061950684,0.7160882353782654,general_sample
95,BRD-K05647501,0.2291751652956009,-0.06926438212394714,general_sample
96,BRD-K78636275,0.22891822457313538,0.7736002206802368,general_sample
97,ditolylguanidine,0.2276442050933838,1.7872586250305176,general_sample
98,BRD-K12683703,0.22574575245380402,-0.5894231200218201,general_sample
99,BRD-K42197878,0.22489723563194275,0.9392799139022827,general_sample
100,ranitidine,0.2243157923221588,1.0414822101593018,negative_control
101,BRD-K00812396,0.2204073816537857,1.7750279903411865,general_sample
102,SA-1921783,0.21941909193992615,0.7298216223716736,general_sample
103,BRD-K57756744,0.21836763620376587,1.2867426872253418,general_sample
104,oprozomib,0.2171071171760559,1.1919209957122803,general_sample
105,astemizole,0.2156534045934677,1.7033143043518066,negative_control
106,BRD-K01977318,0.21503891050815582,1.926210641860962,general_sample
107,neostigmine,0.20658856630325317,1.2066024541854858,general_sample
108,BRD-K86997557,0.2063712477684021,1.7264163494110107,general_sample
109,BRD-K07276035,0.20610132813453674,0.22332103550434113,general_sample
110,BRD-K42733037,0.20607754588127136,0.4705517292022705,general_sample
111,BRD-K88092133,0.20329439640045166,1.5231980085372925,general_sample
112,BRD-K07464613,0.19792267680168152,0.9103862047195435,general_sample
113,BRD-K03463440,0.19763417541980743,0.04750436544418335,general_sample
114,U-54494A,0.19699649512767792,0.6771597266197205,general_sample
115,BRD-K95995661,0.19657522439956665,0.9159876704216003,general_sample
116,BRD-K35234011,0.19374209642410278,1.016001582145691,general_sample
117,BRD-A13914662,0.1926717460155487,0.49716946482658386,general_sample
118,BRD-K87426499,0.19177326560020447,-0.050703004002571106,general_sample
119,BRD-K80747759,0.19016335904598236,-0.5651810765266418,general_sample
120,BRD-K23154136,0.18987241387367249,2.289987802505493,general_sample
121,BRD-K52971552,0.18887174129486084,0.9786604046821594,general_sample
122,BRD-K15259924,0.1882244050502777,1.4186360836029053,general_sample
123,BRD-K60703528,0.18806274235248566,0.40015730261802673,general_sample
124,BRD-K27744061,0.1859944462776184,2.612982749938965,general_sample
125,BRD-K19416218,0.18407133221626282,1.7156975269317627,general_sample
126,loratadine,0.18328134715557098,2.494800090789795,negative_control
127,BRD-K27711805,0.18229132890701294,0.4912426173686981,general_sample
128,BRD-K67727634,0.17958897352218628,-0.022484712302684784,general_sample
129,BRD-K08995626,0.17850513756275177,3.004214286804199,general_sample
130,BRD-K76321890,0.17720356583595276,-0.8629432320594788,general_sample
131,PD-0325901,0.1763416975736618,1.1065287590026855,general_sample
132,BRD-K92028820,0.1763390302658081,0.864924430847168,general_sample
133,BRD-K58096890,0.17460352182388306,1.0638632774353027,general_sample
134,clotrimazole,0.17379066348075867,1.719211459159851,negative_control
135,terbinafine,0.1734161376953125,1.7575925588607788,negative_control
136,BRD-K82925070,0.17324930429458618,2.892310619354248,general_sample
137,BRD-K36820092,0.17034576833248138,0.4257924556732178,general_sample
138,BRD-K99628932,0.1687491536140442,0.9402509927749634,general_sample
139,aliskiren,0.1675613820552826,0.6590442657470703,general_sample
140,BRD-K93880770,0.16621443629264832,1.163874864578247,general_sample
141,BRD-K11989341,0.16608819365501404,0.6260548233985901,general_sample
142,BRD-K06714535,0.16518470644950867,1.6651201248168945,general_sample
143,BRD-K38588505,0.1649388074874878,0.26500213146209717,general_sample
144,BRD-K90705745,0.163993239402771,0.8484952449798584,general_sample
145,BRD-A41228941,0.16353529691696167,0.19634002447128296,general_sample
146,BRD-K04009734,0.16288873553276062,2.185487747192383,general_sample
147,AZD-6482,0.16243045032024384,1.668942928314209,general_sample
148,BRD-K30659453,0.1615477204322815,0.7147446274757385,general_sample
149,BRD-K50120786,0.161424919962883,2.1996657848358154,general_sample
150,BRD-K29635534,0.16122522950172424,0.5763481855392456,general_sample
151,BRD-K58072864,0.16102036833763123,1.7533352375030518,general_sample
152,pomalidomide,0.16026929020881653,1.1876976490020752,related_mechanism
153,BRD-K08482401,0.16006913781166077,1.2936341762542725,general_sample
154,BRD-K38320477,0.1577380746603012,2.0174200534820557,general_sample
155,BRD-K62768824,0.1574127972126007,0.2853902280330658,general_sample
156,BRD-K15672523,0.15602652728557587,0.25686198472976685,general_sample
157,BRD-K57064803,0.15426436066627502,2.142756223678589,general_sample
158,demeclocycline,0.15402083098888397,1.8052453994750977,general_sample
159,BRD-K81312543,0.15399408340454102,0.9155179858207703,general_sample
160,BRD-K65395273,0.15261712670326233,1.9891328811645508,general_sample
161,BRD-K91269653,0.15187959372997284,1.9947938919067383,general_sample
162,BRD-K98997045,0.15097758173942566,0.6952972412109375,general_sample
163,BRD-K44036769,0.14995774626731873,0.2860259413719177,general_sample
164,BRD-K69886508,0.14784830808639526,1.4674654006958008,general_sample
165,BRD-K01528688,0.1477918177843094,1.2374709844589233,general_sample
166,BRD-K45200389,0.14763033390045166,0.9359119534492493,general_sample
167,diphenhydramine,0.14630556106567383,1.6897326707839966,negative_control
168,BRD-K98710661,0.1454104781150818,0.5531234741210938,general_sample
169,BRD-K21635943,0.14415626227855682,1.7998664379119873,general_sample
170,sildenafil,0.14332857728004456,0.24974015355110168,related_mechanism
171,BRD-K14356681,0.14244668185710907,0.1876475214958191,general_sample
172,BRD-K46936109,0.1424178034067154,1.5194870233535767,general_sample
173,TH-302,0.14157085120677948,0.3173200488090515,general_sample
174,caffeine,0.14126121997833252,2.3276991844177246,negative_control
175,BRD-K53443165,0.14010101556777954,1.1625938415527344,general_sample
176,BRD-K73388776,0.139877051115036,-0.3698955178260803,general_sample
177,BRD-K64520484,0.1375540792942047,0.7576441764831543,general_sample
178,norethindrone,0.13644839823246002,1.541637659072876,negative_control
179,BRD-K13626871,0.13602501153945923,1.4089312553405762,general_sample
180,BRD-K72972600,0.13439995050430298,1.1684551239013672,general_sample
181,prednisolone,0.13360020518302917,0.8050864338874817,related_mechanism
182,BRD-K72232421,0.13345623016357422,2.274737596511841,general_sample
183,BRD-A43885598,0.1329154670238495,2.1677091121673584,general_sample
184,loperamide,0.13224346935749054,1.2183666229248047,negative_control
185,BRD-K09487323,0.13214272260665894,2.15812611579895,general_sample
186,BRD-K13307254,0.13211864233016968,1.0333926677703857,general_sample
187,BRD-K93541117,0.13047276437282562,2.168461322784424,general_sample
188,BRD-K40230514,0.12915246188640594,0.6537739038467407,general_sample
189,BRD-K07400331,0.12912264466285706,1.7710614204406738,general_sample
190,BRD-A78236793,0.12736168503761292,1.1413218975067139,general_sample
191,BRD-K95241801,0.12640994787216187,0.00014099478721618652,general_sample
192,BRD-K58023987,0.1262451410293579,0.5590131878852844,general_sample
193,BRD-K87669574,0.12599524855613708,1.7269186973571777,general_sample
194,BRD-K74553461,0.12537837028503418,2.184779644012451,general_sample
195,pipamperone,0.12477646768093109,0.1865198016166687,general_sample
196,JNJ-7706621,0.12447348982095718,0.35190898180007935,general_sample
197,BRD-K52183630,0.12413982301950455,2.428985118865967,general_sample
198,BRD-K57490754,0.12371955066919327,0.41090428829193115,general_sample
199,BRD-K72692763,0.12352791428565979,0.3076161742210388,general_sample
200,enilconazole,0.12276123464107513,1.0041255950927734,general_sample
201,BRD-K81524996,0.12215909361839294,0.6418701410293579,general_sample
202,BRD-K73155123,0.1192801296710968,0.6843189001083374,general_sample
203,BRD-K33528640,0.11878877878189087,0.5734832286834717,general_sample
204,BRD-K38181288,0.11808028817176819,1.7954599857330322,general_sample
205,QX-314,0.11777613312005997,2.060868501663208,general_sample
206,doxycycline,0.11709427833557129,1.192191243171692,negative_control
207,BRD-K68504618,0.11684578657150269,2.608350992202759,general_sample
208,levonorgestrel,0.11591199040412903,1.626094937324524,negative_control
209,itraconazole,0.11584744602441788,-0.09887504577636719,negative_control
210,BRD-K14483137,0.11480832099914551,1.6506483554840088,general_sample
211,BRD-K75990826,0.11396902799606323,0.9468180537223816,general_sample
212,VTP-27999,0.11371782422065735,0.8909273147583008,general_sample
213,BRD-K03235359,0.11317900568246841,2.4507906436920166,general_sample
214,diazepam,0.11256343871355057,1.7679884433746338,general_sample
215,simvastatin,0.11168932914733887,1.3542425632476807,related_mechanism
216,BRD-K38373457,0.11087027192115784,0.11042767763137817,general_sample
217,SB-258585,0.1105894148349762,0.9937275648117065,general_sample
218,azithromycin,0.11050024628639221,0.09130436182022095,negative_control
219,BRD-K97955841,0.11018981784582138,0.5305709838867188,general_sample
220,BRD-K97717522,0.10845574736595154,0.4835914969444275,general_sample
221,thalidomide,0.10836213827133179,2.0089573860168457,related_mechanism
222,reserpic-acid,0.10757994651794434,1.4694583415985107,general_sample
223,BRD-K51644197,0.10701952129602432,0.9039517641067505,general_sample
224,anastrozole,0.10358912497758865,0.9844931960105896,general_sample
225,BRD-K23961390,0.10208642482757568,-0.3048904538154602,general_sample
226,BRD-K82469533,0.10029269754886627,1.1784133911132812,general_sample
227,BRD-K68325500,0.0993058979511261,1.217383861541748,general_sample
228,verapamil,0.09837277233600616,1.61649489402771,general_sample
229,BRD-K00504156,0.09703031927347183,2.15120267868042,general_sample
230,BRD-A57107094,0.09696315228939056,2.0873100757598877,general_sample
231,BRD-K92333822,0.09657244384288788,0.3130739629268646,general_sample
232,BRD-K89675250,0.09552998840808868,1.096104621887207,general_sample
233,BRD-K20151898,0.09535171091556549,1.663360834121704,general_sample
234,BRD-K34811324,0.09506288915872574,1.636451005935669,general_sample
235,hydrocortisone,0.09483426809310913,1.3085203170776367,related_mechanism
236,BRD-K04232710,0.09364677965641022,0.9871090650558472,general_sample
237,BRD-K16539011,0.09267415851354599,2.0138421058654785,general_sample
238,lenalidomide,0.09157396852970123,1.7614586353302002,related_mechanism
239,dapivirine,0.08917832374572754,1.1204332113265991,general_sample
240,BRD-K82935485,0.0889597237110138,1.5348076820373535,general_sample
241,fluconazole,0.08861995488405228,0.7705867886543274,negative_control
242,miconazole,0.08847332000732422,0.3530352711677551,negative_control
243,BRD-K04643052,0.08728811889886856,1.8453972339630127,general_sample
244,trimethoprim,0.08714093267917633,1.5980050563812256,negative_control
245,BRD-K59887251,0.08359691500663757,-0.2983150780200958,general_sample
246,BRD-K97641878,0.08290493488311768,1.6386921405792236,general_sample
247,BRD-K36516410,0.08052213490009308,1.1813796758651733,general_sample
248,BRD-K63431240,0.08046489953994751,0.8348743915557861,general_sample
249,BRD-K07850148,0.0801025852560997,1.1315404176712036,general_sample
250,ketoconazole,0.07924821227788925,-0.2652745544910431,negative_control
251,BRD-K60994920,0.07906623929738998,1.9567651748657227,general_sample
252,medroxyprogesterone-acetate,0.07816928625106812,1.2908352613449097,negative_control
253,BRD-K42610174,0.07811297476291656,2.000000476837158,general_sample
254,BRD-K91339294,0.07743799686431885,1.6037771701812744,general_sample
255,BRD-K47885451,0.07666181027889252,1.7753000259399414,general_sample
256,BRD-K31042955,0.07525031268596649,-0.02010802924633026,general_sample
257,BRD-K85763971,0.07524567097425461,0.8542464971542358,general_sample
258,BRD-K73360774,0.07404312491416931,0.08928011357784271,general_sample
259,laropiprant,0.07321711629629135,1.2876667976379395,general_sample
260,BRD-K34462187,0.07217635214328766,2.635417938232422,general_sample
261,BRD-K00930335,0.07178701460361481,1.4565761089324951,general_sample
262,BRD-K98113345,0.07017907500267029,0.6807817220687866,general_sample
263,BRD-K39685946,0.06969957798719406,0.20744098722934723,general_sample
264,ketocholesterol,0.06865204125642776,1.517796516418457,general_sample
265,BRD-K54687541,0.06733538955450058,1.6019880771636963,general_sample
266,BRD-K89554882,0.06596627831459045,0.9116415977478027,general_sample
267,adrenosterone,0.06559927761554718,1.6499176025390625,general_sample
268,oseltamivir-carboxylate,0.06034604460000992,1.8670696020126343,general_sample
269,BRD-K33514849,0.06033096835017204,0.9989179968833923,general_sample
270,BRD-K62265198,0.0597817488014698,2.0923120975494385,general_sample
271,BRD-K01520595,0.059522368013858795,1.1388102769851685,general_sample
272,BRD-K75965029,0.05909409373998642,0.8850012421607971,general_sample
273,BRD-K60379529,0.056600529700517654,1.3942689895629883,general_sample
274,BRD-K77323800,0.05628868564963341,0.76136714220047,general_sample
275,BRD-K93200353,0.05566142499446869,1.367753028869629,general_sample
276,BRD-K39337865,0.0547766387462616,1.8628408908843994,general_sample
277,BRD-K34412442,0.05267806351184845,1.960115909576416,general_sample
278,BRD-K41866979,0.05012091249227524,0.5144319534301758,general_sample
279,ticagrelor,0.049006469547748566,0.0014074146747589111,related_mechanism
280,BRD-K40829514,0.04817928373813629,0.4225776195526123,general_sample
281,BRD-K02257023,0.046159256249666214,1.8649888038635254,general_sample
282,BRD-K47105324,0.042336881160736084,0.6837743520736694,general_sample
283,BRD-K79992300,0.04170645773410797,1.2891095876693726,general_sample
284,BRD-K43905345,0.040275897830724716,2.065195322036743,general_sample
285,BRD-K42269438,0.03933650255203247,1.3552615642547607,general_sample
286,BRD-K56349799,0.03727919980883598,1.6540254354476929,general_sample
287,dexamethasone-acetate,0.03663018345832825,1.0805904865264893,general_sample
288,BRD-K27675859,0.03387710824608803,1.9398986101150513,general_sample
289,SB-525334,0.032205577939748764,1.5904217958450317,general_sample
290,rucaparib,0.03211560472846031,0.8603106141090393,general_sample
291,BRD-K45787391,0.031139448285102844,0.741227388381958,general_sample
292,pregnenolone,0.030906977131962776,1.5815171003341675,general_sample
293,BRD-K19645992,0.03016829863190651,1.7404652833938599,general_sample
294,BRD-K50309272,0.028783636167645454,1.5358946323394775,general_sample
295,dexamethasone,0.027089979499578476,0.6470061540603638,related_mechanism
296,torin-1,0.02660956233739853,-0.252296507358551,general_sample
297,BRD-K08246588,0.02257409133017063,2.5512869358062744,general_sample
298,BRD-K87400432,0.02154897153377533,1.3216978311538696,general_sample
299,AV-608,0.020470259711146355,1.0707037448883057,general_sample
1 rank drug P_binder affinity inclusion_reason
2 1 trichostatin-a 0.9995425343513489 -2.8145930767059326 related_mechanism
3 2 vorinostat 0.9994102716445923 -1.736063003540039 related_mechanism
4 3 panobinostat 0.9985321760177612 -2.5815885066986084 related_mechanism
5 4 belinostat 0.9969940185546875 -2.1257152557373047 related_mechanism
6 5 BG-1003 0.9969587326049805 -1.7902384996414185 general_sample
7 6 scriptaid 0.9953755140304565 -1.604792833328247 related_mechanism
8 7 mocetinostat 0.9910330772399902 -1.1003236770629883 related_mechanism
9 8 entinostat 0.9900848865509033 -0.66916424036026 related_mechanism
10 9 apicidin 0.9881076812744141 -2.1283297538757324 related_mechanism
11 10 BRD-K14666757 0.9683372974395752 -0.6549662351608276 general_sample
12 11 JW55 0.9362592697143555 -0.4662295877933502 general_sample
13 12 valproic-acid 0.8981399536132812 0.37430477142333984 related_mechanism
14 13 FIT 0.8313940763473511 0.08768215775489807 general_sample
15 14 hydroxyurea 0.7578531503677368 1.246307611465454 ground_truth
16 15 ibuprofen 0.7412509918212891 2.238396167755127 related_mechanism
17 16 sulforaphane 0.739348292350769 0.3284870982170105 related_mechanism
18 17 BRD-K10302728 0.7058488130569458 -0.9450978636741638 general_sample
19 18 BRD-K61285042 0.6548928022384644 0.49822238087654114 general_sample
20 19 ciprofibrate 0.633934736251831 1.9368321895599365 general_sample
21 20 KI-16425 0.6012023091316223 0.6640514731407166 general_sample
22 21 curcumin 0.5989675521850586 1.486403226852417 related_mechanism
23 22 BRD-K29660619 0.5905249118804932 0.12171633541584015 general_sample
24 23 resveratrol 0.5783771276473999 1.2722764015197754 related_mechanism
25 24 BRD-K27824357 0.564523458480835 0.1906198263168335 general_sample
26 25 tadalafil 0.5615900754928589 0.007123969495296478 related_mechanism
27 26 BRD-K46241566 0.5496933460235596 0.8938988447189331 general_sample
28 27 BRD-K99633092 0.5473401546478271 -0.44378313422203064 general_sample
29 28 BRD-K32389477 0.5432510375976562 -0.9505497813224792 general_sample
30 29 talnetant 0.5365580320358276 -0.4235907196998596 general_sample
31 30 montelukast 0.5170086622238159 0.7837215662002563 related_mechanism
32 31 tetracaine 0.514898419380188 0.486468642950058 general_sample
33 32 SA-1480001 0.5129876732826233 -0.14114731550216675 general_sample
34 33 lawsone 0.5126880407333374 1.3275636434555054 general_sample
35 34 quercetin 0.5112301111221313 0.35112306475639343 related_mechanism
36 35 BRD-K67328514 0.47897130250930786 1.6453043222427368 general_sample
37 36 glutamine 0.4580795168876648 2.2292144298553467 ground_truth
38 37 romidepsin 0.438159316778183 -0.6780526638031006 related_mechanism
39 38 BRD-K19362120 0.43379056453704834 -0.38182151317596436 general_sample
40 39 rifaximin 0.43118005990982056 -0.007878035306930542 general_sample
41 40 palmitoylethanolamide 0.4253748655319214 1.5332996845245361 general_sample
42 41 D-64131 0.4243965148925781 1.8345916271209717 general_sample
43 42 deferasirox 0.414570152759552 0.8550795912742615 related_mechanism
44 43 BRD-K39379309 0.39516061544418335 1.2569950819015503 general_sample
45 44 cetirizine 0.39126813411712646 1.497683048248291 negative_control
46 45 decitabine 0.3905729651451111 0.9013112783432007 related_mechanism
47 46 ingenol 0.38832157850265503 1.2636841535568237 general_sample
48 47 BRD-K02558072 0.38382846117019653 1.3527982234954834 general_sample
49 48 lestaurtinib 0.37580811977386475 0.5706255435943604 general_sample
50 49 BRD-K22546959 0.373577356338501 1.4228181838989258 general_sample
51 50 sulfasalazine 0.3713478446006775 0.9489234089851379 related_mechanism
52 51 brompheniramine 0.36528241634368896 0.7533001899719238 general_sample
53 52 SKI-II 0.3633918762207031 1.0488131046295166 general_sample
54 53 BRD-K03142004 0.3538649380207062 0.4557762145996094 general_sample
55 54 miltefosine 0.3524576723575592 1.3234755992889404 general_sample
56 55 lidocaine 0.3505249321460724 2.832113265991211 negative_control
57 56 omeprazole 0.3403707444667816 1.4137210845947266 negative_control
58 57 BW-B70C 0.34008413553237915 1.2555820941925049 general_sample
59 58 azacitidine 0.33303695917129517 0.8310854434967041 related_mechanism
60 59 KO-143 0.33238181471824646 -0.9562602043151855 general_sample
61 60 trioxsalen 0.33212581276893616 2.046276569366455 general_sample
62 61 dexchlorpheniramine 0.3283562660217285 1.02620530128479 general_sample
63 62 ciprofloxacin 0.32668250799179077 0.26640501618385315 negative_control
64 63 aspirin 0.3254982829093933 2.339493751525879 related_mechanism
65 64 BRD-K55966666 0.3211105465888977 -0.2134701907634735 general_sample
66 65 carisoprodol 0.3141220510005951 1.6034519672393799 general_sample
67 66 tetracycline 0.31255578994750977 1.2801803350448608 negative_control
68 67 atorvastatin 0.3122830092906952 0.5527983903884888 related_mechanism
69 68 BRD-K19105325 0.3045218586921692 -0.2390911877155304 general_sample
70 69 BRD-A27640568 0.3026970326900482 1.965691328048706 general_sample
71 70 phenolphthalein 0.3001948595046997 0.9219919443130493 general_sample
72 71 BRD-K71182391 0.29757264256477356 0.5220360159873962 general_sample
73 72 BRD-K38061943 0.2891416549682617 0.14858180284500122 general_sample
74 73 BRD-K93445052 0.28817978501319885 0.7619435787200928 general_sample
75 74 halofantrine 0.28806358575820923 0.008057385683059692 general_sample
76 75 BRD-K16912444 0.28658565878868103 -0.0714123547077179 general_sample
77 76 BRD-K39431601 0.2835044860839844 -0.3456823229789734 general_sample
78 77 LY-341495 0.27582740783691406 0.44341373443603516 general_sample
79 78 tyrphostin-A9 0.2754404842853546 1.5046072006225586 general_sample
80 79 BRD-K87449690 0.26641374826431274 2.289837121963501 general_sample
81 80 BRD-K87720600 0.2651839256286621 0.2896602153778076 general_sample
82 81 fexofenadine 0.26415905356407166 1.2466082572937012 negative_control
83 82 BRD-K33284065 0.2630389928817749 0.6950460076332092 general_sample
84 83 ITE 0.257363498210907 1.146105170249939 general_sample
85 84 amoxicillin 0.25568023324012756 1.8630526065826416 negative_control
86 85 BRD-K45889441 0.25448158383369446 0.6300027966499329 general_sample
87 86 BRD-K52524742 0.25103557109832764 1.058586835861206 general_sample
88 87 methotrexate 0.24424436688423157 1.9891445636749268 general_sample
89 88 BRD-K67470788 0.24184325337409973 1.50880765914917 general_sample
90 89 ethinyl-estradiol 0.24175500869750977 1.410076379776001 negative_control
91 90 lisinopril 0.2400914877653122 1.5881357192993164 general_sample
92 91 BRD-K93411257 0.23802407085895538 -0.2541484236717224 general_sample
93 92 BRD-K71353154 0.23799994587898254 0.5835225582122803 general_sample
94 93 cyclazosin 0.23158416152000427 0.03154781460762024 general_sample
95 94 BRD-K74271701 0.23076415061950684 0.7160882353782654 general_sample
96 95 BRD-K05647501 0.2291751652956009 -0.06926438212394714 general_sample
97 96 BRD-K78636275 0.22891822457313538 0.7736002206802368 general_sample
98 97 ditolylguanidine 0.2276442050933838 1.7872586250305176 general_sample
99 98 BRD-K12683703 0.22574575245380402 -0.5894231200218201 general_sample
100 99 BRD-K42197878 0.22489723563194275 0.9392799139022827 general_sample
101 100 ranitidine 0.2243157923221588 1.0414822101593018 negative_control
102 101 BRD-K00812396 0.2204073816537857 1.7750279903411865 general_sample
103 102 SA-1921783 0.21941909193992615 0.7298216223716736 general_sample
104 103 BRD-K57756744 0.21836763620376587 1.2867426872253418 general_sample
105 104 oprozomib 0.2171071171760559 1.1919209957122803 general_sample
106 105 astemizole 0.2156534045934677 1.7033143043518066 negative_control
107 106 BRD-K01977318 0.21503891050815582 1.926210641860962 general_sample
108 107 neostigmine 0.20658856630325317 1.2066024541854858 general_sample
109 108 BRD-K86997557 0.2063712477684021 1.7264163494110107 general_sample
110 109 BRD-K07276035 0.20610132813453674 0.22332103550434113 general_sample
111 110 BRD-K42733037 0.20607754588127136 0.4705517292022705 general_sample
112 111 BRD-K88092133 0.20329439640045166 1.5231980085372925 general_sample
113 112 BRD-K07464613 0.19792267680168152 0.9103862047195435 general_sample
114 113 BRD-K03463440 0.19763417541980743 0.04750436544418335 general_sample
115 114 U-54494A 0.19699649512767792 0.6771597266197205 general_sample
116 115 BRD-K95995661 0.19657522439956665 0.9159876704216003 general_sample
117 116 BRD-K35234011 0.19374209642410278 1.016001582145691 general_sample
118 117 BRD-A13914662 0.1926717460155487 0.49716946482658386 general_sample
119 118 BRD-K87426499 0.19177326560020447 -0.050703004002571106 general_sample
120 119 BRD-K80747759 0.19016335904598236 -0.5651810765266418 general_sample
121 120 BRD-K23154136 0.18987241387367249 2.289987802505493 general_sample
122 121 BRD-K52971552 0.18887174129486084 0.9786604046821594 general_sample
123 122 BRD-K15259924 0.1882244050502777 1.4186360836029053 general_sample
124 123 BRD-K60703528 0.18806274235248566 0.40015730261802673 general_sample
125 124 BRD-K27744061 0.1859944462776184 2.612982749938965 general_sample
126 125 BRD-K19416218 0.18407133221626282 1.7156975269317627 general_sample
127 126 loratadine 0.18328134715557098 2.494800090789795 negative_control
128 127 BRD-K27711805 0.18229132890701294 0.4912426173686981 general_sample
129 128 BRD-K67727634 0.17958897352218628 -0.022484712302684784 general_sample
130 129 BRD-K08995626 0.17850513756275177 3.004214286804199 general_sample
131 130 BRD-K76321890 0.17720356583595276 -0.8629432320594788 general_sample
132 131 PD-0325901 0.1763416975736618 1.1065287590026855 general_sample
133 132 BRD-K92028820 0.1763390302658081 0.864924430847168 general_sample
134 133 BRD-K58096890 0.17460352182388306 1.0638632774353027 general_sample
135 134 clotrimazole 0.17379066348075867 1.719211459159851 negative_control
136 135 terbinafine 0.1734161376953125 1.7575925588607788 negative_control
137 136 BRD-K82925070 0.17324930429458618 2.892310619354248 general_sample
138 137 BRD-K36820092 0.17034576833248138 0.4257924556732178 general_sample
139 138 BRD-K99628932 0.1687491536140442 0.9402509927749634 general_sample
140 139 aliskiren 0.1675613820552826 0.6590442657470703 general_sample
141 140 BRD-K93880770 0.16621443629264832 1.163874864578247 general_sample
142 141 BRD-K11989341 0.16608819365501404 0.6260548233985901 general_sample
143 142 BRD-K06714535 0.16518470644950867 1.6651201248168945 general_sample
144 143 BRD-K38588505 0.1649388074874878 0.26500213146209717 general_sample
145 144 BRD-K90705745 0.163993239402771 0.8484952449798584 general_sample
146 145 BRD-A41228941 0.16353529691696167 0.19634002447128296 general_sample
147 146 BRD-K04009734 0.16288873553276062 2.185487747192383 general_sample
148 147 AZD-6482 0.16243045032024384 1.668942928314209 general_sample
149 148 BRD-K30659453 0.1615477204322815 0.7147446274757385 general_sample
150 149 BRD-K50120786 0.161424919962883 2.1996657848358154 general_sample
151 150 BRD-K29635534 0.16122522950172424 0.5763481855392456 general_sample
152 151 BRD-K58072864 0.16102036833763123 1.7533352375030518 general_sample
153 152 pomalidomide 0.16026929020881653 1.1876976490020752 related_mechanism
154 153 BRD-K08482401 0.16006913781166077 1.2936341762542725 general_sample
155 154 BRD-K38320477 0.1577380746603012 2.0174200534820557 general_sample
156 155 BRD-K62768824 0.1574127972126007 0.2853902280330658 general_sample
157 156 BRD-K15672523 0.15602652728557587 0.25686198472976685 general_sample
158 157 BRD-K57064803 0.15426436066627502 2.142756223678589 general_sample
159 158 demeclocycline 0.15402083098888397 1.8052453994750977 general_sample
160 159 BRD-K81312543 0.15399408340454102 0.9155179858207703 general_sample
161 160 BRD-K65395273 0.15261712670326233 1.9891328811645508 general_sample
162 161 BRD-K91269653 0.15187959372997284 1.9947938919067383 general_sample
163 162 BRD-K98997045 0.15097758173942566 0.6952972412109375 general_sample
164 163 BRD-K44036769 0.14995774626731873 0.2860259413719177 general_sample
165 164 BRD-K69886508 0.14784830808639526 1.4674654006958008 general_sample
166 165 BRD-K01528688 0.1477918177843094 1.2374709844589233 general_sample
167 166 BRD-K45200389 0.14763033390045166 0.9359119534492493 general_sample
168 167 diphenhydramine 0.14630556106567383 1.6897326707839966 negative_control
169 168 BRD-K98710661 0.1454104781150818 0.5531234741210938 general_sample
170 169 BRD-K21635943 0.14415626227855682 1.7998664379119873 general_sample
171 170 sildenafil 0.14332857728004456 0.24974015355110168 related_mechanism
172 171 BRD-K14356681 0.14244668185710907 0.1876475214958191 general_sample
173 172 BRD-K46936109 0.1424178034067154 1.5194870233535767 general_sample
174 173 TH-302 0.14157085120677948 0.3173200488090515 general_sample
175 174 caffeine 0.14126121997833252 2.3276991844177246 negative_control
176 175 BRD-K53443165 0.14010101556777954 1.1625938415527344 general_sample
177 176 BRD-K73388776 0.139877051115036 -0.3698955178260803 general_sample
178 177 BRD-K64520484 0.1375540792942047 0.7576441764831543 general_sample
179 178 norethindrone 0.13644839823246002 1.541637659072876 negative_control
180 179 BRD-K13626871 0.13602501153945923 1.4089312553405762 general_sample
181 180 BRD-K72972600 0.13439995050430298 1.1684551239013672 general_sample
182 181 prednisolone 0.13360020518302917 0.8050864338874817 related_mechanism
183 182 BRD-K72232421 0.13345623016357422 2.274737596511841 general_sample
184 183 BRD-A43885598 0.1329154670238495 2.1677091121673584 general_sample
185 184 loperamide 0.13224346935749054 1.2183666229248047 negative_control
186 185 BRD-K09487323 0.13214272260665894 2.15812611579895 general_sample
187 186 BRD-K13307254 0.13211864233016968 1.0333926677703857 general_sample
188 187 BRD-K93541117 0.13047276437282562 2.168461322784424 general_sample
189 188 BRD-K40230514 0.12915246188640594 0.6537739038467407 general_sample
190 189 BRD-K07400331 0.12912264466285706 1.7710614204406738 general_sample
191 190 BRD-A78236793 0.12736168503761292 1.1413218975067139 general_sample
192 191 BRD-K95241801 0.12640994787216187 0.00014099478721618652 general_sample
193 192 BRD-K58023987 0.1262451410293579 0.5590131878852844 general_sample
194 193 BRD-K87669574 0.12599524855613708 1.7269186973571777 general_sample
195 194 BRD-K74553461 0.12537837028503418 2.184779644012451 general_sample
196 195 pipamperone 0.12477646768093109 0.1865198016166687 general_sample
197 196 JNJ-7706621 0.12447348982095718 0.35190898180007935 general_sample
198 197 BRD-K52183630 0.12413982301950455 2.428985118865967 general_sample
199 198 BRD-K57490754 0.12371955066919327 0.41090428829193115 general_sample
200 199 BRD-K72692763 0.12352791428565979 0.3076161742210388 general_sample
201 200 enilconazole 0.12276123464107513 1.0041255950927734 general_sample
202 201 BRD-K81524996 0.12215909361839294 0.6418701410293579 general_sample
203 202 BRD-K73155123 0.1192801296710968 0.6843189001083374 general_sample
204 203 BRD-K33528640 0.11878877878189087 0.5734832286834717 general_sample
205 204 BRD-K38181288 0.11808028817176819 1.7954599857330322 general_sample
206 205 QX-314 0.11777613312005997 2.060868501663208 general_sample
207 206 doxycycline 0.11709427833557129 1.192191243171692 negative_control
208 207 BRD-K68504618 0.11684578657150269 2.608350992202759 general_sample
209 208 levonorgestrel 0.11591199040412903 1.626094937324524 negative_control
210 209 itraconazole 0.11584744602441788 -0.09887504577636719 negative_control
211 210 BRD-K14483137 0.11480832099914551 1.6506483554840088 general_sample
212 211 BRD-K75990826 0.11396902799606323 0.9468180537223816 general_sample
213 212 VTP-27999 0.11371782422065735 0.8909273147583008 general_sample
214 213 BRD-K03235359 0.11317900568246841 2.4507906436920166 general_sample
215 214 diazepam 0.11256343871355057 1.7679884433746338 general_sample
216 215 simvastatin 0.11168932914733887 1.3542425632476807 related_mechanism
217 216 BRD-K38373457 0.11087027192115784 0.11042767763137817 general_sample
218 217 SB-258585 0.1105894148349762 0.9937275648117065 general_sample
219 218 azithromycin 0.11050024628639221 0.09130436182022095 negative_control
220 219 BRD-K97955841 0.11018981784582138 0.5305709838867188 general_sample
221 220 BRD-K97717522 0.10845574736595154 0.4835914969444275 general_sample
222 221 thalidomide 0.10836213827133179 2.0089573860168457 related_mechanism
223 222 reserpic-acid 0.10757994651794434 1.4694583415985107 general_sample
224 223 BRD-K51644197 0.10701952129602432 0.9039517641067505 general_sample
225 224 anastrozole 0.10358912497758865 0.9844931960105896 general_sample
226 225 BRD-K23961390 0.10208642482757568 -0.3048904538154602 general_sample
227 226 BRD-K82469533 0.10029269754886627 1.1784133911132812 general_sample
228 227 BRD-K68325500 0.0993058979511261 1.217383861541748 general_sample
229 228 verapamil 0.09837277233600616 1.61649489402771 general_sample
230 229 BRD-K00504156 0.09703031927347183 2.15120267868042 general_sample
231 230 BRD-A57107094 0.09696315228939056 2.0873100757598877 general_sample
232 231 BRD-K92333822 0.09657244384288788 0.3130739629268646 general_sample
233 232 BRD-K89675250 0.09552998840808868 1.096104621887207 general_sample
234 233 BRD-K20151898 0.09535171091556549 1.663360834121704 general_sample
235 234 BRD-K34811324 0.09506288915872574 1.636451005935669 general_sample
236 235 hydrocortisone 0.09483426809310913 1.3085203170776367 related_mechanism
237 236 BRD-K04232710 0.09364677965641022 0.9871090650558472 general_sample
238 237 BRD-K16539011 0.09267415851354599 2.0138421058654785 general_sample
239 238 lenalidomide 0.09157396852970123 1.7614586353302002 related_mechanism
240 239 dapivirine 0.08917832374572754 1.1204332113265991 general_sample
241 240 BRD-K82935485 0.0889597237110138 1.5348076820373535 general_sample
242 241 fluconazole 0.08861995488405228 0.7705867886543274 negative_control
243 242 miconazole 0.08847332000732422 0.3530352711677551 negative_control
244 243 BRD-K04643052 0.08728811889886856 1.8453972339630127 general_sample
245 244 trimethoprim 0.08714093267917633 1.5980050563812256 negative_control
246 245 BRD-K59887251 0.08359691500663757 -0.2983150780200958 general_sample
247 246 BRD-K97641878 0.08290493488311768 1.6386921405792236 general_sample
248 247 BRD-K36516410 0.08052213490009308 1.1813796758651733 general_sample
249 248 BRD-K63431240 0.08046489953994751 0.8348743915557861 general_sample
250 249 BRD-K07850148 0.0801025852560997 1.1315404176712036 general_sample
251 250 ketoconazole 0.07924821227788925 -0.2652745544910431 negative_control
252 251 BRD-K60994920 0.07906623929738998 1.9567651748657227 general_sample
253 252 medroxyprogesterone-acetate 0.07816928625106812 1.2908352613449097 negative_control
254 253 BRD-K42610174 0.07811297476291656 2.000000476837158 general_sample
255 254 BRD-K91339294 0.07743799686431885 1.6037771701812744 general_sample
256 255 BRD-K47885451 0.07666181027889252 1.7753000259399414 general_sample
257 256 BRD-K31042955 0.07525031268596649 -0.02010802924633026 general_sample
258 257 BRD-K85763971 0.07524567097425461 0.8542464971542358 general_sample
259 258 BRD-K73360774 0.07404312491416931 0.08928011357784271 general_sample
260 259 laropiprant 0.07321711629629135 1.2876667976379395 general_sample
261 260 BRD-K34462187 0.07217635214328766 2.635417938232422 general_sample
262 261 BRD-K00930335 0.07178701460361481 1.4565761089324951 general_sample
263 262 BRD-K98113345 0.07017907500267029 0.6807817220687866 general_sample
264 263 BRD-K39685946 0.06969957798719406 0.20744098722934723 general_sample
265 264 ketocholesterol 0.06865204125642776 1.517796516418457 general_sample
266 265 BRD-K54687541 0.06733538955450058 1.6019880771636963 general_sample
267 266 BRD-K89554882 0.06596627831459045 0.9116415977478027 general_sample
268 267 adrenosterone 0.06559927761554718 1.6499176025390625 general_sample
269 268 oseltamivir-carboxylate 0.06034604460000992 1.8670696020126343 general_sample
270 269 BRD-K33514849 0.06033096835017204 0.9989179968833923 general_sample
271 270 BRD-K62265198 0.0597817488014698 2.0923120975494385 general_sample
272 271 BRD-K01520595 0.059522368013858795 1.1388102769851685 general_sample
273 272 BRD-K75965029 0.05909409373998642 0.8850012421607971 general_sample
274 273 BRD-K60379529 0.056600529700517654 1.3942689895629883 general_sample
275 274 BRD-K77323800 0.05628868564963341 0.76136714220047 general_sample
276 275 BRD-K93200353 0.05566142499446869 1.367753028869629 general_sample
277 276 BRD-K39337865 0.0547766387462616 1.8628408908843994 general_sample
278 277 BRD-K34412442 0.05267806351184845 1.960115909576416 general_sample
279 278 BRD-K41866979 0.05012091249227524 0.5144319534301758 general_sample
280 279 ticagrelor 0.049006469547748566 0.0014074146747589111 related_mechanism
281 280 BRD-K40829514 0.04817928373813629 0.4225776195526123 general_sample
282 281 BRD-K02257023 0.046159256249666214 1.8649888038635254 general_sample
283 282 BRD-K47105324 0.042336881160736084 0.6837743520736694 general_sample
284 283 BRD-K79992300 0.04170645773410797 1.2891095876693726 general_sample
285 284 BRD-K43905345 0.040275897830724716 2.065195322036743 general_sample
286 285 BRD-K42269438 0.03933650255203247 1.3552615642547607 general_sample
287 286 BRD-K56349799 0.03727919980883598 1.6540254354476929 general_sample
288 287 dexamethasone-acetate 0.03663018345832825 1.0805904865264893 general_sample
289 288 BRD-K27675859 0.03387710824608803 1.9398986101150513 general_sample
290 289 SB-525334 0.032205577939748764 1.5904217958450317 general_sample
291 290 rucaparib 0.03211560472846031 0.8603106141090393 general_sample
292 291 BRD-K45787391 0.031139448285102844 0.741227388381958 general_sample
293 292 pregnenolone 0.030906977131962776 1.5815171003341675 general_sample
294 293 BRD-K19645992 0.03016829863190651 1.7404652833938599 general_sample
295 294 BRD-K50309272 0.028783636167645454 1.5358946323394775 general_sample
296 295 dexamethasone 0.027089979499578476 0.6470061540603638 related_mechanism
297 296 torin-1 0.02660956233739853 -0.252296507358551 general_sample
298 297 BRD-K08246588 0.02257409133017063 2.5512869358062744 general_sample
299 298 BRD-K87400432 0.02154897153377533 1.3216978311538696 general_sample
300 299 AV-608 0.020470259711146355 1.0707037448883057 general_sample

29
docs/structure_binding_notes.md
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@@ -160,8 +160,35 @@ model. The screen mishandles non-standard chemotypes (prodrugs, macrocycles).
The screening pipeline is validated. Next: run the full set (incl. the 240 random + negatives) to The screening pipeline is validated. Next: run the full set (incl. the 240 random + negatives) to
hunt for NON-obvious HDAC2 binders (the actual discovery run), ~$15-20. hunt for NON-obvious HDAC2 binders (the actual discovery run), ~$15-20.
## Step 7 — Full 300-drug discovery screen vs HDAC2 (2026-06-26)
`modal run gpu/modal_app.py::screen` — 299 drugs co-folded vs HDAC2 (+Zn), ranked by P(binder).
Corrected pipeline: 1 MSA query (computed once, reused), 299/299 screened, 0 failures, ~$5-8.
**Scale validation:** HDAC inhibitors occupy ranks 1-9 (trichostatin-A, vorinostat, panobinostat,
belinostat, scriptaid, mocetinostat, entinostat, apicidin; all ≥0.99), weak valproic-acid demoted
to 0.90. The pilot held at 300.
**DECISIVE — specificity (the thing connectivity could NOT do):** the best-scoring negative
control is cetirizine at **rank 44, P=0.39**. All 26 negative controls (antifungals,
antihistamines, antibiotics, hormones) rank low — co-folding REJECTS the unrelated drugs. This is
the exact failure mode that sank the connectivity approach (negative controls ranked top there);
structure-based binding has the specificity expression-connectivity fundamentally lacked.
**Discovery hits (non-obvious high-P binders):** BG-1003 (rank 5, P=0.997, general_sample),
BRD-K14666757 (10, 0.968), JW55 (11, 0.936, a tankyrase inhibitor), FIT (13, 0.831). 11 drugs
score P>0.9 = 8 known HDAC inhibitors + 3 non-obvious. BG-1003 is the standout — a "random" LINCS
compound scoring as a near-certain HDAC2 binder above several known inhibitors.
**Honest caveats:** BG-1003 may be a known HDAC inhibitor that landed in the random sample (→
validation, not novelty) — needs an identity/literature check before any claim. Several hits are
unannotated BRD tool compounds. Binding != efficacy. The screen still mishandles prodrugs/
macrocycles (romidepsin-type false negatives). Full ranking: docs/results/screen_HDAC2_full.csv.
## Next steps ## Next steps
- [ ] Full screen (300 drugs) vs HDAC2 — discovery run for non-obvious binders. - [ ] Identity-check BG-1003 and the BRD hits (ChEMBL/literature): known HDAC binders or novel?
- [ ] Pose-RMSD the top non-obvious hits (geometry sanity, like vorinostat).
- [ ] Extend the screen to other validated HbF/hemoglobin targets; integrate with the expression layer.
- [ ] Investigate PKR: allosteric site may need the full assembly / better pocket definition. - [ ] Investigate PKR: allosteric site may need the full assembly / better pocket definition.
- [ ] Phase 2 screen: rank the ~300-drug set against HDAC2 (the validated target) by P(binder); - [ ] Phase 2 screen: rank the ~300-drug set against HDAC2 (the validated target) by P(binder);
positive-control recovery test at screen scale. positive-control recovery test at screen scale.