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sequence | contacts_11A
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sequence |
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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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