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PubChem

Look up any chemical from a workflow.

actions
10

Actions

Steps a workflow can run in PubChem.

  • Find a compoundTurn whatever names a chemical into the chemical itself. Give a name, a brand, a CAS number, a structure drawn as SMILES or InChI, an InChI key, a molecular formula or a PubChem CID, and get back the formula, the weight, the structure as text, the properties that decide how a molecule behaves, and a plain language description of what it actually is. This is the step to put first: everything else here takes the same kinds of value, so once a spreadsheet column or a form answer has been run through this, the rest of the workflow knows exactly which molecule it is dealing with.
  • Get compound detailsBuild one table of chemistry across a whole list of compounds. Hand it the column out of a spreadsheet, a form or an earlier step, up to a hundred at a time, tick the facts you want, and get a row per compound with those columns filled in. Anything PubChem cannot place comes back in its own list rather than being quietly dropped, so a run over real data says exactly which rows need a human. This is the enrichment step: names in, formulas, weights, solubility and drug likeness out.
  • Find similar compoundsFind the molecules that look like one you already have. PubChem compares the structures themselves rather than their names, so this surfaces the analogue nobody thought to name similarly: a generic beside a brand, a metabolite beside its parent, a cheaper reagent beside an expensive one. Set how alike they have to be, from 50 for a loose family resemblance to 95 and above for near twins. The compound you asked about always comes back first and is flagged, so a workflow can drop it in one step.
  • Search by structureSearch a hundred million compounds by shape rather than by name. Draw a fragment and ask what contains it, to find every molecule built around a particular ring or group. Or name a whole molecule and ask what it is part of, to find the salts, esters and mixtures it turns up in. Or ask for the exact structure, which is how to check whether something has already been catalogued. Or ask for everything sharing a molecular formula, which is how to find the isomers that weigh the same and behave differently.
  • List a compound's namesOne chemical goes by hundreds of names: a trade name, a systematic name, a catalogue code, the spelling a supplier uses and the spelling a regulator uses. This lists them all for one compound, so two records that look unrelated can be matched up. CAS registry numbers are pulled out into their own list, because that is the number an order form or a safety sheet asks for and it is otherwise buried among the names.
  • List a compound's referencesFind out who has written about a chemical and who holds it. Returns the papers that mention it, linked straight to PubMed; the patents that claim it, linked to Google Patents; the databases and suppliers that carry a record for it, with links back to those records; and the catalogue numbers they file it under. Use it to gauge how well studied something is before committing to it, to watch a competitor's patent activity, or to find where else to buy a reagent. Well studied compounds have six figures of patents, so the counts come back in full and the lists are trimmed.
  • List a compound's test resultsRead what a chemical has actually been tested against and what each experiment concluded. PubChem holds over a million biological assays, and a widely studied compound appears in thousands of them: this returns a row per result with the experiment, the verdict, the protein it was tested against and the potency where one was measured, plus a tally of how the verdicts break down. Filter to the active results to see only where something worked, which is how to tell a molecule with a real biological story from one that has simply been screened a lot.
  • Get a bioassayRead one biological experiment in full: what it set out to measure, the protein or organism it was aimed at, how it was run, how many compounds went through it and how many came out active, and which those were. The description and protocol are the researchers' own words, so this is where a result stops being a number and becomes something you can judge. Assay numbers come from 'List a compound's test results' or from looking up a gene.
  • Look up a gene, protein, pathway or organismWork the other way round: start from the biology and find the chemistry aimed at it. Name a gene, a protein, a biological pathway or an organism and get what it is, what else it is called, which species it belongs to, and every experiment PubChem holds that was aimed at it. Those experiment numbers feed straight into 'Get a bioassay', which is how to go from 'we are interested in this gene' to the compounds that have actually been tested against it.
  • Download a structure fileGet the molecule itself as a file, ready to hand to something else. The structure file is what modelling, docking and drawing software reads, flat for a diagram or as a computed three dimensional shape for anything that cares about how the molecule sits. The image is a clean drawing of the structure, for dropping into a report, an email or a slide. Both come back as a real file a later step can attach or save.

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