User: entropy

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entropy50
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Posts by entropy

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Comment: C: For virtual screning, finding bioactivity data for the protein targets with no b
... Thank you very much for your kind and detailed answer. I think, my question was not detailed enough as your second answer is quite different than I expect. Let me explain in more detail. My main goal is to find hit compounds, from Chembl or similar other databases like ZINC , which binds to my tar ...
written 6 months ago by entropy50
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... PacBio would be great. ...
written 6 months ago by entropy50
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For virtual screning, finding bioactivity data for the protein targets with no bioactivity data available?
... Hi, Using Chembl bioactivity data (mainly with SMILES), I trained my Deep Learning model for hit detection of my target proteins via virtual screning. However, Chembl does not have compound bioactivity data for all the proteins. I have some proteins of interest that is not available either in Chemb ...
compound drug target ml protein hit detection written 7 months ago by entropy50 • updated 6 months ago by matteoferla20
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PacBio end-to-end pipeline advise
... Dear all, Could you please advise an end-to-end PacBio pipeline if available? There are too many pages I visited but I could not find a single end-to-end command line pipeline that takes raw reads as input and performs iso-seq analysis and aligns to a reference genome and get annotations and perfo ...
isoseq alignment pipeline pacbio rna-seq written 7 months ago by entropy50
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Comment: C: Convertion from Uniprot ID to Gene Symbol does not work well.
... Thanks. I think that answers my question. Is there a way to scan all at once instead of looping per database? ...
written 9 months ago by entropy50
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Comment: C: Convertion from Uniprot ID to Gene Symbol does not work well.
... Thanks. It looks there exist some. I just tried and got this:"1,370 out of 1,433 identifiers from UniProtKB AC/ID were successfully mapped to 1,092 Gene name IDs.". For example I got this: A7MBE0 SLC22A1 O08537 Esr2 and so on... Actually, I uploaded 15K IDs but received only that ...
written 9 months ago by entropy50 • updated 9 months ago by genomax85k
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Convertion from Uniprot ID to Gene Symbol does not work well.
... This seems to be a basic process but somehow I could not find the best answer yet. I am trying to convert Uniprot IDs into Gene Symbols. I run this code but about 1/4 of my list returns NA, Is there a better way to get the full conversion right? uniprots[1:5] . # "A0QVH7" "A0R666" "A0SYQ0" "A3 ...
genome rna-seq sequencing written 9 months ago by entropy50 • updated 9 months ago by ATpoint36k
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Comment: C: Is there a LIST of available drugs and their target proteins to download?
... Thanks. I got the impression that there is limitation for commercial usage of it? Is there not any other source with no limitations? ...
written 9 months ago by entropy50
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Is there a LIST of available drugs and their target proteins to download?
... Is there a downloadable LIST of available drugs and their target proteins? For example like this: Protein Drug --------- --------- CXCR4 Ibalizumab Protein2 Drug2 and so on It may also include not approved drugs. I have a large list of targets and want to see "programmatically" whic ...
drug targets drug repurposing proteins drugs written 9 months ago by entropy50 • updated 9 months ago by Kevin Blighe61k
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Answer: A: Expression plots of some genes of interest from scRNA data for each library
... I ended up doing this manually. ...
written 10 months ago by entropy50

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Student 9 months ago, asked a question with at least 3 up-votes. For Is there a LIST of available drugs and their target proteins to download?

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