Comments (4)
Shen-Lab
commented on June 6, 2024
Thank you for your interest in our package. For the mapping between internal DeepAffinity IDs and external public IDs, you can find in cleared data description (https://github.com/Shen-Lab/DeepAffinity/blob/master/data/README.md) that, for each pair of compound and protein, we gave DeepAffinity Protein ID, UniProt Protein ID, DeepAffinity Compound ID, PubChem CID, and the affinity measurement of the pair. The mapping is not currently provided in the desired format but could be easily converted using the provided files.
For the 881-digit PubMed fingerprint, I believe that we retrieved it for each compound from PubChem using the compound's CID. @AstroSign Could you please provide some more details? Was it done through some PubChem API, say PubChemPy?
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AstroSign
commented on June 6, 2024
In terms of getting fingerprints of compounds, we downloaded data in SDF
format based on CID from
https://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi . They also provide
other APIs which can be found here:
https://pubchemdocs.ncbi.nlm.nih.gov/downloads . In the SDF file, the
fingerprint features are stored in Base64-encoded format under the tag
"PUBCHEM_CACTVS_SUBSKEYS". To understand the meaning of each digit and how
to decode, you may refer to their document (
https://pubchemdocs.ncbi.nlm.nih.gov/data-specification).
Thanks.
…On Wed, Jan 27, 2021 at 1:46 PM Shen Lab at Texas A&M University < ***@***.***> wrote:
Thank you for your interest in our package. For the mapping between
internal DeepAffinity IDs and external public IDs, you can find in cleared
data description (
https://github.com/Shen-Lab/DeepAffinity/blob/master/data/README.md)
that, for each pair of compound and protein, we gave DeepAffinity Protein
ID, UniProt Protein ID, DeepAffinity Compound ID, PubChem CID, and the
affinity measurement of the pair. The mapping is not currently provided in
the desired format but could be easily converted using the provided files.
For the 881-digit PubMed fingerprint, I believe that we retrieved it for
each compound from PubChem using the compound's CID. @AstroSign
<https://github.com/AstroSign> Could you please provide some more
details? Was it done through some PubChem API, say PubChemPy?
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hyojin0912
commented on June 6, 2024
Thank you for your comments.
I got PubChem Fingerprint from SDF file.
But if I transform Base 64 encoded vector to binary bit vector, it's length is 920 not 881.
Could you describe me how to select exact fingerprint vector?
For example, Lorlatinib's (PubChem CID=71731823) fingerprint ->
Base64 Encoded Fingerprint = AAADceB7sQAAAAAAAAAAAAAAAAAAAWAAAAA8QAAAAAAAAAAB8AAAHwAYAAAADBzhng4/tpNIFAC6Bzd3dASyjCk14CAY2CE/TNiO5vLE9duXvSjkzhPY6a+62KOOgAAAAAAQAAAAAAAAACAAAAAAAAAAAA==
Binary Bit Vector = 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 1 1 1 0 0 0 0 0 0 1 1 1 1 1 0 1 1 1 1 0 1 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 0 1 0 1 0 0 1 0 0 0 0 0 1 1 0 1 0 1 1 0 0 1 0 0 1 1 1 1 0 0 1 0 1 1 1 1 0 0 0 0 0 0 1 1 1 1 1 1 0 0 1 0 0 1 0 0 0 1 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 1 1 0 0 0 0 0 1 1 1 0 1 1 0 0 1 1 1 0 1 1 1 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 1 1 0 0 1 0 1 0 0 1 0 0 0 1 1 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 1 1 0 1 1 1 0 0 0 0 1 0 1 0 0 0 1 1 1 0 1 0 1 1 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 0 1 1 1 0 1 0 0 1 1 1 1 1 0 0 0 0 0 1 1 1 1 1 1 1 0 0 1 1 0 0 0 1 1 0 1 0 0 1 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 1 1 1 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 0 1 1 1 1 1 1 0 1 0 0 0 0 1 1 1 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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AstroSign
commented on June 6, 2024
As I mentioned earlier, you may refer to the last two paragraphs in
https://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt
. As it described, "The fingerprint is, therefore, 111 bytes in length (888
bits), which includes *padding of seven bits* at the end to complete the
last byte. *A four-byte prefix*, containing the bit length of the
fingerprint (881 bits)".
Thanks.
…On Wed, Mar 3, 2021 at 11:19 PM Sonhyojin ***@***.***> wrote:
Thank you for your comments.
I got PubChem Fingerprint from SDF file.
But if I transform Base 64 encoded vector to binary bit vector, it's
length is 920 not 881.
Could you describe me how to select exact fingerprint vector?
For example, Lorlatinib's (PubChem CID=71731823) fingerprint ->
Base64 Encoded Fingerprint =
AAADceB7sQAAAAAAAAAAAAAAAAAAAWAAAAA8QAAAAAAAAAAB8AAAHwAYAAAADBzhng4/tpNIFAC6Bzd3dASyjCk14CAY2CE/TNiO5vLE9duXvSjkzhPY6a+62KOOgAAAAAAQAAAAAAAAACAAAAAAAAAAAA==
Binary Bit Vector = 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0
0 1 1 1 0 0 0 0 0 0 1 1 1 1 1 0 1 1 1 1 0 1 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0
0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0
0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0
0 0 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0
1 0 1 0 1 0 0 1 0 0 0 0 0 1 1 0 1 0 1 1 0 0 1 0 0 1 1 1 1 0 0 1 0 1 1 1 1 0
0 0 0 0 0 1 1 1 1 1 1 0 0 1 0 0 1 0 0 0 1 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 1 0 1 0 1 1 0 0 0 0 0 1 1 1 0 1 1 0 0 1 1 1 0 1 1 1 0 0 0 1
0 1 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 1 1 0 0 1 0 1 0 0 1
0 0 0 1 1 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 1 1 0 1
1 1 0 0 0 0 1 0 1 0 0 0 1 1 1 0 1 0 1 1 0 1 1 1 0 0 0 0 1 1 0 0 1 0 0 0 1 0
0 0 1 0 0 0 0 0 1 1 1 0 1 0 0 1 1 1 1 1 0 0 0 0 0 1 1 1 1 1 1 1 0 0 1 1 0 0
0 1 1 0 1 0 0 1 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 0 1
1 1 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 1 0 0 1 1 1 1 1 1 0 1 0
0 0 0 1 1 1 0 0 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 1 0 1 1 1 0 0 0 1 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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Related Issues (15)
- Data HOT 8
- About 'uniprot.human.scratch_outputs.w_sps.tab_corrected' file HOT 2
- model number in output
- Is the tool Mac compatible?
- Can't create environment
- Both Training and Testing with my own dataset.
- Typrerror when running joint-Model_test.py HOT 1
- Trained Models HOT 6
- Pubchem fingerprints HOT 2
- why tflearn? HOT 2
- Checkpoint for ki dataset HOT 2
- Generating the protein SPS representation HOT 12
- No BindingDB_All.tsv exists. HOT 2
- Why should the number of SAP representation protein sequence file lines and the number of Canonical compound SMILE file lines match? HOT 2
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