User: cdsouthan

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cdsouthan1.8k
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Curator at Guide to PHARMACOLOGY database  See http://www.linkedin.com/in/cdsouthan

Posts by cdsouthan

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Comment: C: Ensembl protein counts
... Seeing as I may finally get round to revising https://www.ncbi.nlm.nih.gov/pubmed/28529709 I would appreciate if Ben or anyone else could send me sequences for what are now 562 read through human proteins ...
written 12 weeks ago by cdsouthan1.8k
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Answer: A: Transmembrane domain protein structure
... InterPro - but the unintegrated signatures at the bottom ...
written 12 weeks ago by cdsouthan1.8k
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Comment: C: Converting Affymetrix Probes To Gene Ids
... 4 years on so this will never happen? ...
written 7 months ago by cdsouthan1.8k
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Answer: A: 5th International Conference on Integrative Biology, June 19-21, 2017 at London,
... Oh dear, this is a predatory conference. It probably slipped through moderation but should be removed ...
written 8 months ago by cdsouthan1.8k
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Comment: C: 5th International Conference on Integrative Biology, June 19-21, 2017 at London,
... Oh dear, a predatory conference, probably slipped through moderation (fix?) ...
written 8 months ago by cdsouthan1.8k
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Counting human proteins with at least 1 authentic bound ligand compound in PDB
... This seems to be a difficult question to get a clean answer to. We need it as background to our binding domain mapping project http://synpharm.guidetopharmacology.org/ This PDBe query http://www.ebi.ac.uk/pdbe/entry/search/index?organism_synonyms:%22Homo%20sapiens%20(Human)%22&view=compou ...
pdb ligands human proteins written 8 months ago by cdsouthan1.8k • updated 7 months ago by Biostar ♦♦ 20
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Answer: A: An Up-To-Date, Parse-Able And Free Antibody Database
... The Human Protein Atlas http://www.proteinatlas.org/ more or less exactly fits the answer for antibodies histochemically binding to their actual target proteins (with the caveats explained in their publications) They are linked with https://www.antibodypedia.com/ (that Bioz seems to be a ...
written 8 months ago by cdsouthan1.8k
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Comment: C: HGNC cross-references in UniProt
... Thanks for all the comments, I managed the review in the end "Last rolls of the yoyo: Assessing the human canonical protein count [version 1; referees: awaiting peer review]" https://f1000research.com/articles/6-448/v1 feedback welcome ...
written 9 months ago by cdsouthan1.8k
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Comment: C: HGNC cross-references in UniProt
... OK, thanks, but the biological/curation issue behind the numbers above is as follows: It looks like Swiss-Prot have included a large number of proteins (in the order of ~ 500-800) that HGNC are not classifying as protein-coding. The largest categories I think (by manual inspection of matches fro ...
written 10 months ago by cdsouthan1.8k
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Answer: A: isoforms and the definition of a protein
... Isoform is such an ambiguous qualifier it should be banned (but we know this is spitting in the wind). It has ancient origins back in the days of protein isoelectric focusing where band-splits were just conveniently named isoforms (even though this splitting was dominated by carbohydrate side chain ...
written 11 months ago by cdsouthan1.8k

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