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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7193,
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578,
579,
582,
584,
586,
587,
5... |
PKYTKSVLKKGDKTNFPKKGDVVHCWYTGTLQDGTVFDTNIQTSAKKKKNAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLTFEVELVDIDLEHH | C=CCC1/C=C(\C)CC(C)CC(OC)C2OC(O)(C(=O)C(=O)N3CCCCC3C(=O)OC(/C(C)=C/C3CCC(O)C(OC)C3)C(C)C(O)CC1=O)C(C)CC2OC | 0.2 | 6.69897 | 0.18772 | [
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19042,
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19554,
27661,
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2... | [
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13910,
13922,
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1... | [
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2103,
2607,
2608,
2609,
3121... |
PPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSLRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHRVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAKMDWIFHTI | COC(=O)Nc1ccc2c(c1)OCCc1cc(-c3nncn3-c3ccccc3Cl)sc1-2 | 0.001 | 9 | 1.404165 | [
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410143,
410144... | [
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394791... | [
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368165,
368167... |
ALVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRISCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRCGHH | NC(=O)c1ccc(Cc2ccccc2)cc1-c1cccc(CCC(=O)O)c1 | 0.012 | 7.920819 | 0.833654 | [
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9230... | [
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2066,
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10... | [
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1038,
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1047,
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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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410113,
410114,
410115... | [
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395290... | [
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368131... |
HKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALG | CC(=O)CC(c1ccccc1)c1c(O)c2ccccc2oc1=O | 2.9 | 5.537602 | -0.42624 | [
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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) |
End of preview. Expand in Data Studio
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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