User: Wolf Ihlenfeldt

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Posts by Wolf Ihlenfeldt

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Is there any way to map ChEMBL compound IDs to KEGG Drug IDs?
... Cactvs toolkit (www.xemistry.com/academic, free software for academic users only): a) Python pycactvs>Ens('CHEMBL113').E_KEGG_DRUG_ID 'D00528' b) Tcl cactvs>ens get CHEMBL113 E_KEGG_DRUG_ID D00528 ...
written 11 days ago by Wolf Ihlenfeldt70
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Comment: C: How to convert chemdraw file in CDX format either into Mol2 or SDF format?
... Yes, of course. xxx dummy characters to fill it to 20 xxx ...
written 3 months ago by Wolf Ihlenfeldt70
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Answer: A: How to convert chemdraw file in CDX format either into Mol2 or SDF format?
... You can for example use the CACTVS toolkit (free for academic users, www.xemistry.com/academic, documentation at www.xemistry.com/docs): Minimal sample command line input with Python interface: pycactvs>Molfile.Write('myfile.sdf',Molfile.Read('myfile.cdx')) Sybyl Mol2 is a mandatory 3D fo ...
written 3 months ago by Wolf Ihlenfeldt70
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Answer: A: Is it theoretically possible to text mine symptoms following chemical exposure?
... My suggestion would be to start your project with safety data sheets instead of full papers or abstracts. They are shorter and more formalized in their content and structure. ...
written 5 months ago by Wolf Ihlenfeldt70
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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 18 months ago by Wolf Ihlenfeldt70
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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 23 months ago by Wolf Ihlenfeldt70
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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 2.1 years ago by Wolf Ihlenfeldt70
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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 2.2 years ago by Wolf Ihlenfeldt70
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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 7.9 years ago by Wolf Ihlenfeldt70
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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 8.1 years ago by Wolf Ihlenfeldt70

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