User: Wolf Ihlenfeldt

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Posts by Wolf Ihlenfeldt

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Convert multiple .mol files from the KEGG database to pdb.
... mol2 files are not mol files. The reported messages look like the inputs are 2D mol files, and there are failures to generate 3D coordinates. Converted 3D mol2 to and from 3D pdb is a trivial exercise in comparison. If the compounds are reasonably well known (i.e. they are in PubChem), I would sugg ...
written 8 months ago by Wolf Ihlenfeldt40
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Answer: A: KEGG Pathway - A circle includes many compounds
... The tooltip name simply enumerates a couple of possible compounds (actually, one generic name for a variable and two common instantiations for specific fixed s) for different values of in the bracket [] of the structure drawing. ...
written 13 months ago by Wolf Ihlenfeldt40
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Answer: A: Converting between drug identifier formats
... This is easily done with the Cactvs Cheminformatics Toolkit (visit www.xemistry.com/academic for free academic packages, it includes both a loadable Python module and a stand-alone Python interpreter with chemistry extensions). The toolkit can decode the three IDs you are using (and many more) into ...
written 16 months ago by Wolf Ihlenfeldt40
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Answer: A: Retrieving MeSH Pharmacological Classification for Compounds in pubChem
... You cannot do this via PUG alone. You need to perform some multi-level Entrez EUtils wrangling for this. Two possibilities: a) Learn and understand EUtils and the relationships between the various NCBI databases to some depth b) Use our Cheminformatics toolkit (www.xemistry.com/academic for free ...
written 16 months ago by Wolf Ihlenfeldt40
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Answer: A: Parsing Pubchem Compound Records
... As far as I know, the only tool outside NCBI which can parse the native ASN.1 PubChem data is the CACTVS Chemoinformatics toolkit (www.xemistry.com/academic for free academic versions). The toolkit has tight links into PubChem. For example, to get a structure with all associated standard data via a ...
written 7.1 years ago by Wolf Ihlenfeldt40
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Answer: A: How To Retrieve The Crossreferences To Other Databases From Pubchem Compounds
... Easily done with the CACTVS toolkit (www.xemistry.com/academic has a free version for academic use). Script snippet: foreach cid $cidlist { set eh [ens create $cid] if {![catch {ens get $eh E_CHEBI_ID} id]} { puts "ChEBI: $id" } # same for other identifiers of interest, the only one ...
written 7.3 years ago by Wolf Ihlenfeldt40
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Comment: C: How To Retrieve The Crossreferences To Other Databases From Pubchem Compounds
... Easily done with the CACTVS toolkt (www.xemistry.com/academic has a free version for academic use). Script snippet: foreach cid $cidlist { set eh [ens create $cid] if {![catch {ens get $eh E_CHEBI_ID} id]} { puts "ChEBI: $id" } same for other identifiers of interest, the only one from your lis ...
written 7.3 years ago by Wolf Ihlenfeldt40
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Answer: A: Given Several Compound Reference Numbers, How To Get The Molecular Files
... The most convenient and powerful way to access both the quoted name resolver and PubChem is by means of the Cactvs toolkit (www.xemistry.com/academic, free for academic users). Unfortunately, your example does not work, since N5023 is not a registered name. But using this tool you can get your stru ...
written 7.7 years ago by Wolf Ihlenfeldt40

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