seq
stringlengths
24
4.72k
smiles
stringlengths
4
443
affinity_uM
float32
0
400k
neg_log10_affinity_M
float32
0.4
15.2
affinity
float32
-3.14
4.69
contacts_5A
sequence
contacts_8A
sequence
contacts_11A
sequence
contacts_15A
sequence
NLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT
CSCCC(NC(=O)C(C)NC(=O)C(C)NC(=O)C(CCCC[NH3+])NC(=O)CNC(=O)C(Cc1ccccc1)NC(=O)C(Cc1ccccc1)NC(=O)C(CC(N)=O)NC(=O)C(CO)NC(=O)C(CCSC)NC(=O)C(CCSC)NC(=O)C(CC(N)=O)NC(=O)CNC(=O)C([NH3+])CCCC[NH3+])C(=O)NC(CC(N)=O)C(=O)NC(CCCC[NH3+])C(=O)O
2.3
5.638272
-0.37302
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0.2
6.69897
0.18772
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PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSLRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHRVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAKMDWIFHTI
COC(=O)Nc1ccc2c(c1)OCCc1cc(-c3nncn3-c3ccccc3Cl)sc1-2
0.001
9
1.404165
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439830, 439831, 439833, 439834, 439845, 439847, 439848, 439849, 439850, 439855, 439856, 440321, 440322, 440323, 440326, 440328, 440329, 440331, 440332, 440333, 440335, 440337, 440360, 440833, 440834, 440835, 440838, 440840, 440841, 440843, 440844, 440849, 440872, 440873, 441345, 441346, 441347, 441350, 441352, 441353, 441355, 441356, 441357, 441359, 441361, 441364, 441365, 441392, 448513, 448514, 448515, 448518, 448520, 448521, 448523, 448529, 450049, 450050, 450051, 450054, 450056, 450057, 450059, 450060, 450061, 450063, 450065, 450068, 450069, 450070, 450071, 450096, 450561, 450562, 450563, 450566, 450568, 452097, 452098, 452099, 452102, 452104, 452105, 452107, 452108, 452109, 452111, 452113, 452116, 452117, 452144, 452609, 452610, 458773, 460308, 460309, 460310, 462344, 462345, 462347, 462348, 462349, 462351, 462353, 462356, 462357, 462358, 462359, 462361, 462362, 462365, 462367, 462368, 462369, 462370, 462373, 462375, 462379, 462381, 462383, 462384, 464405, 464406, 464407, 464409, 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469516, 469517, 469519, 469521, 469524, 469525, 469526, 469527, 469529, 469530, 469533, 469535, 469536, 469537, 469538, 469541, 469543, 469544, 469545, 469546, 469547, 469549, 469551, 469552, 470017, 470018, 470019, 470022, 470024, 470025, 470027, 470028, 470029, 470031, 470033, 470036, 470037, 470038, 470039, 470041, 470042, 470045, 470047, 470048, 470049, 470050, 470053, 470055, 470056, 470057, 470058, 470059, 470061, 470063, 470064, 470529, 470530, 470531, 470534, 470536, 470537, 470539, 470540, 470541, 470543, 470545, 470548, 470549, 470550, 470551, 470553, 470554, 470557, 470559, 470560, 470561, 470562, 470565, 470567, 470568, 470569, 470570, 470571, 470573, 470575, 470576, 471041, 471042, 471043, 471046, 471048, 471049, 471051, 471052, 471053, 471055, 471057, 471060, 471061, 471062, 471063, 471065, 471066, 471069, 471071, 471072, 471073, 471074, 471077, 471079, 471080, 471081, 471082, 471083, 471085, 471087, 471088, 471553, 471554, 471555, 471558, 471560, 471561, 471563, 471564, 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474635, 474636, 474637, 474639, 474641, 474644, 474645, 474646, 474647, 474649, 474650, 474671, 474672, 475137, 475138, 475139, 475142, 475144, 475145, 475147, 475148, 475149, 475151, 475153, 475156, 475157, 475158, 475159, 475161, 475162, 475165, 475167, 475183, 475184, 475649, 475650, 475651, 475654, 475656, 475657, 475659, 475660, 475661, 475663, 475665, 475668, 475669, 475670, 475671, 475673, 475674, 475677, 475679, 475680, 475681, 475682, 475685, 475687, 475688, 475689, 475690, 475691, 475693, 475695, 475696, 476161, 476162, 476163, 476166, 476168, 476169, 476171, 476172, 476173, 476175, 476177, 476180, 476181, 476182, 476183, 476185, 476186, 476189, 476191, 476192, 476193, 476194, 476197, 476199, 476200, 476201, 476202, 476203, 476205, 476207, 476208, 476673, 476674, 476675, 476678, 476680, 476681, 476683, 476684, 476685, 476687, 476689, 476692, 476693, 476694, 476695, 476697, 476698, 476701, 476703, 476704, 476705, 476706, 476709, 476711, 476712, 476713, 476714, 476715, 476717, 476719, 476720, 477185, 477186, 477187, 477190, 477192, 477193, 477195, 477196, 477197, 477199, 477201, 477204, 477205, 477206, 477207, 477209, 477210, 477213, 477215, 477216, 477217, 477218, 477221, 477223, 477224, 477225, 477226, 477227, 477229, 477231, 477232, 477704, 477705, 477707, 477708, 477709, 477711, 477713, 477716, 477717, 477718, 477719, 477721, 477722, 477725, 477727, 477728, 477729, 477730, 477733, 477735, 477736, 477737, 477738, 477739, 477741, 477743, 477744, 478219, 478220, 478221, 478223, 478225, 478228, 478229, 478230, 478231, 478233, 478234, 478237, 478239, 478240, 478241, 478242, 478245, 478247, 478248, 478249, 478250, 478251, 478253, 478255, 478256, 478741, 478742, 478743, 478745, 478746, 478749, 478751, 478752, 478753, 478754, 478757, 478759, 478760, 478761, 478762, 478763, 478765, 478767, 478768, 491029, 516640, 517663, 517664, 517665, 517666, 540678, 540712 ]
ALVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRISCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRCGHH
NC(=O)c1ccc(Cc2ccccc2)cc1-c1cccc(CCC(=O)O)c1
0.012
7.920819
0.833654
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PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIF
COc1ncc(-c2ccc3ncnc(-c4cccc(C(=O)N5CCN(C(C)=O)CC5)c4)c3c2)cc1C#N
0.262
6.581699
0.125724
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HKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALG
CC(=O)CC(c1ccccc1)c1c(O)c2ccccc2oc1=O
2.9
5.537602
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"MNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNK(...TRUNCATED)
CCCC(=O)Nc1cc(NS(=O)(=O)c2cccs2)cc(-c2csc(=O)[nH]2)c1
0.79
6.102373
-0.127672
[19970,19971,19972,19975,19977,19978,19980,19981,19987,19993,19995,19996,19997,19998,20017,20482,204(...TRUNCATED)
[18973,19458,19460,19463,19495,19969,19970,19971,19972,19975,19977,19978,19980,19981,19983,19984,199(...TRUNCATED)
[1025,16897,16898,16899,16903,18434,18435,18436,18439,18441,18459,18460,18461,18462,18946,18947,1894(...TRUNCATED)
[513,514,515,516,519,521,522,524,525,527,528,531,535,545,546,549,551,552,553,556,558,561,1025,1026,1(...TRUNCATED)
"SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEAWLEILMIGLVWRSMEHPGKLLF(...TRUNCATED)
CCCCOC(=O)c1ccc(O)cc1
2.11
5.675717
-0.353225
[19970,21510,21513,21515,21517,21518,23054,23057,23563,23565,23566,23567,25101,25102,25103,25105,251(...TRUNCATED)
[11793,19465,19969,19970,19971,19972,19973,19974,19977,19979,19981,20998,21001,21003,21005,21006,215(...TRUNCATED)
[10255,10257,10766,10767,10769,10771,11278,11279,11281,11283,11787,11789,11790,11791,11793,11795,117(...TRUNCATED)
[9233,9742,9743,9745,9747,9748,10246,10251,10253,10254,10255,10257,10259,10260,10757,10758,10761,107(...TRUNCATED)
"QIDLNVTCRYAGVFHVEKNGRYSISRTEAADLCQAFNSTLPTMDQMKLALSKGFETCRYGFIEGNVVIPRIHPNAICAANHTGVYILVTSNTSHYDTYC(...TRUNCATED)
CC(=O)NC1COC(CO)C(O)C1OC1OC(C(=O)O)C(OC2OC(CO)C(O)C(OC3OC(C(=O)O)C(O)C(O)C3O)C2NC(C)=O)C(O)C1O
428
3.368556
-1.572912
[10790,10791,10793,10799,10803,10805,10806,10822,10824,10826,10828,10830,10832,10833,10835,10838,113(...TRUNCATED)
[7752,7756,8774,8776,8780,10779,10781,10784,10786,10788,10790,10791,10793,10794,10796,10797,10799,10(...TRUNCATED)
[2632,3652,3654,3656,7733,7734,7736,7737,7746,7748,7750,7752,7754,7756,7760,7761,7763,7766,8264,8268(...TRUNCATED)
[1608,1612,2118,2120,2124,2613,2614,2616,2617,2619,2626,2628,2630,2632,2634,2636,2643,3138,3140,3142(...TRUNCATED)
"AEFSDAVTEETLKKQVAEAWSRRTPFSHEVIVMDMDPFLHCVIPNFIQSQDFLEGLQKELMNLDFHEKYNDLYKFQQSDDLKKRREPHISTLRKILFED(...TRUNCATED)
O=C(O)c1ccnc(C(=O)O)c1
2.3
5.638272
-0.37302
[61953,62977,62979,62983,62988,62990,62993,62997,66055,66057,66058,66059,66060,66062,66065,66067,660(...TRUNCATED)
[36878,36881,36883,37390,37393,37395,38401,38412,38414,38417,38419,38421,39425,39436,39438,39441,394(...TRUNCATED)
[19465,19466,19467,19468,20489,20490,33281,34828,34830,34833,34835,34837,35854,35857,35859,36871,368(...TRUNCATED)
[18442,18953,18954,18955,19457,19459,19461,19463,19465,19466,19467,19468,19470,19473,19475,19477,199(...TRUNCATED)

How to use the data sets

This dataset contains more than 16,000 unique pairs of protein sequences and ligand SMILES with experimentally determined binding affinities and protein-ligand contacts (ligand atom/SMILES token vs. Calpha within 5 Angstrom). These are represented by a list that contains the positions of non-zero elements of the flattened, sparse sequence x smiles tokens (2048x512) matrix. The first and last entries in both dimensions are padded to zero, they correspond to [CLS] and [SEP].

It can be used for fine-tuning a language model.

The data solely uses data from PDBind-cn.

Contacts are calculated at four cut-off distances: 5, 8, 11A and 15A.

Use the already preprocessed data

Load a test/train split using

from datasets import load_dataset
train = load_dataset("jglaser/protein_ligand_contacts",split='train[:90%]')
validation = load_dataset("jglaser/protein_ligand_contacts",split='train[90%:]')

Pre-process yourself

To manually perform the preprocessing, download the data sets from P.DBBind-cn

Register for an account at https://www.pdbbind.org.cn/, confirm the validation email, then login and download

  • the Index files (1)
  • the general protein-ligand complexes (2)
  • the refined protein-ligand complexes (3)

Extract those files in pdbbind/data

Run the script pdbbind.py in a compute job on an MPI-enabled cluster (e.g., mpirun -n 64 pdbbind.py).

Perform the steps in the notebook pdbbind.ipynb

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