- Mar 2017
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pubchemblog.ncbi.nlm.nih.gov pubchemblog.ncbi.nlm.nih.gov
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Therefore, some records in PubChem can persist with outdated (or incorrect) data. To help identify such cases, we are introducing a “legacy” indication for contributors and their records. Please note that this does not mean that data identified as “legacy” is without value.
This might be a trivial question but, would this be the case were certain compounds are not found on some databases but can be found on PubChem? Sooyah
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- Feb 2017
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olcc.ccce.divched.org olcc.ccce.divched.org
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While the InChI representation is normally too complex for a human to decode, it is impossible for even a computer to extract the chemical structure from the InChIKey. therefore, it is important that the InChI repre-sentation is also included in any database.
In instances were chemical structures can't be determined with the provided InChI or InChIKey, are there any tips for searching with an InChI?
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these additional data, coupled with the additional metadata recorded in the SDF format, makes this file format ideal
In what instances is MDL ideal and/or when would you prefer MDL over SDF?
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a key advantage of the Molfile and SDF formats is the inclusion of geomet-ric information regarding the spatial arrangement of atoms in three-dimen-sional space.
You talk of advantages of using both MDL and SDF formats, are there any disadvantages that would make you utilize other formats?
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olcc.ccce.divched.org olcc.ccce.divched.org
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TheMolecular Structure Encoding System, MOSES, fromMolecular Networks (Erlangen, Germany) is a laterdevelopment from Gasteiger’s team.
What features does MOSES have or how does it address the issue delocalization of electrons between more then two atoms?
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olcc.ccce.divched.org olcc.ccce.divched.org
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The chemical formula is straightforward enough, but the connectivity and hydrogen sections require some explanation. The connectivity layer describes chains and branches –for example in the above Propene example, atom 1 is bonded to atom 3, which is bonded to atom 2. In the final example, we have branching, as represented by paren
This explanation further down makes sense, considering that " different implementations interpret SMILES differently", especially for compounds that have the same chemical formula. I was wondering as to how you would get to the right InChI key, starting from a chemical formula.
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