25 Matching Annotations
  1. May 2017
    1. Two-dimensional (2-D) similarity methods

      In the 2D structure similarity below, I wonder how the fingerprint indicate the number of bond. For instance, like C-C bond, how do you know which one since both of them has C-C bond? - Phuc

  2. Apr 2017
    1. In PUG-REST, these three pieces of information are encoded into an URL in the following format:

      I'm guessing these basic piece of information would be similar to the CACTUS chemical resolver URL.-Phuc

    2. https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/180/record/PNG

      I know it through PUG-REST, but how are these generated? same for those link afterward.-Phuc

    3. Entrez Utilities (also called E-Utilities or E-Utils) Power User Gateway (PUG) PUG-SOAP PUG-REST

      Are these suitable with any kind of programmatic platform? -Phuc

  3. Mar 2017

      For the shape tanimoto, can we manually calculated it? Since this is overlapping, is there any relating to the X-Y-Z coordinate in Mol File? -Phuc

    1. MMFF94s

      In case if you curious about MMFF94s. and this might answering my previous question about certain element limitation. -Phuc

    2. Consist of only supported elements (H, C, N, O, F, Si, P, S, Cl, Br, and I).

      So any organometallic compounds such as cis-platin don't have 3D structure? and why we have to set this limit? -Phuc

    1. Biomolecular Interactions and Pathways

      This link should helped answering part of question 3 -Phuc

    1. An Entrez "node" is a collection of data that is grouped together and indexed together

      As an example for searching on Entrez AIDS so like Literature, Health, Genomes, etc are considered as a "node" and little section above that are link within nodes?- Phuc

    1. This “legacy” designation applies to project/contributors that appear to no longer be active, as well as to their individual records.  This designation will help PubChem users quickly identify records that may have out-of-date information and/or hyperlinks.

      This might sound a bit dumb. But, if it's out of date or not really validated, why not just remove it? Phuc

    1. As of February 2017, PubChem’s data are from more than 500 organizations, including government agencies, university labs, pharmaceutical companies, substance vendors, and other databases

      How would Pubchem curate and check the validity of those data coming from different sources? Phuc

    2. Getting the most out of PubChem for virtual screening

      What are other tool for drugs virtual screening in Pubchem beside structure similarities? Phuc

  4. Feb 2017
    1. ANalytical Data Interchange (ANDI)

      Is this type of file recently developed? I have not ever seen this one as the save option in our UALR Agilent GC-MS

    2. <request string="arsinic acid" representation="names">   <data id="1" resolver="name_by_opsin" notation="arsinic acid">     <item id="1" classification="pubchem_iupac_name">arsinic acid</item>     <item id="2" classification="pubchem_substance_synonym">CHEBI:29840</item>     <item id="3" classification="pubchem_substance_synonym">HAsH2O2</item>     <item id="4" classification="pubchem_substance_synonym">[AsH2O(OH)]</item>     <item id="5" classification="pubchem_substance_synonym">arsinic acid</item>     <item id="6" classification="pubchem_substance_synonym">dihydridohydroxidooxidoarsenic</item>   </data> </request>

      How can you pull this string of data? is it from inspection option on the browser? what type of file is this?

    3. chemical metadata (information about chemicals – not chemical data like melting points etc.)

      I need more to clarification about chemical metadata. Like what is it represent if it's not like melting point??

    1. The first block of 14 (out of total 27) characters for anInChIKey encodes core molecular constitution, as de-scribed by formula, connectivity, hydrogen positions andcharge sublayers of the InChI main laye

      Can you search the web with the first block of the InchI key and find all isomer of the compound?

    1. WLN:WiswesserLineNotatio

      I havent encountered this line notation at all. Wonder if is there any database systems still use this as a part of history showcase? (know that it is already out of favor)

    1. Generic structures are commonly used in chemistry texts as well as in chemical patents in which the inventor claims a whole class of related compounds.  Generic structures are more often called “Markush” structures after Dr. Eugene A. Markush, who involved in a legal case which set a precedent in the USA for generic chemical structure patent filing.

      This might sound a bit dumb! Can Inchi be generate from a Markush structure? I know generic structure and Inchi are quite contradicted from each other. Markush can be quite proprietary and InCHI is open science.

    2. c1ccccc1           Benzene (C6H6)

      if there are different substituent group on a benzene. Will SMILE indicate its position such as Ortho, Para, Meta?

    1. MOL files do indicate chirality. However, they can do so in two ways. A “1” or “6” in the fourth field of the bonds table indicates wedged and dashed bonds, respectively. A “1” or “2” in the stereochemistry field of the atom table represents the chirality of a stereocenter.

      Is there any clue on the Mol File that if the structure has more than one chirality center?

    2. As an example, take isopropyl alcohol. SCT I is a connection table representing this compound – or, more specifically, representing this structural formula. Connection tables are not necessarily unique We could draw up other tables of atoms and bonds that represent this compound as well: for example, SCT II and SCT III

      I'm just wonder how this connection table is form? Is it from Morgan algorithm or just randomly assign number for atom?

    1. The Morgan algorithm identifies atoms basedon an extended connectivity value. The atom withthe highest value becomes the first atom in the name,and its neighbors are then listed in descending or-der. Ties are resolved based on additional parame-ters, for example, bond order and atomic number.The original Morgan algorithm did not handle stere-ochemistry; the stereochemically unique naming algo-rithm [stereochemical extension of Morgan algorithm(SEMA)] was developed to handle stereoisomers

      If figure 3 connection table is created based on Morgan algorithm, how would the carbon from the far left is put as the 1st atom not the nitrogen?

    1. Fortunately, this can be done with the Morgan Algorithm18.In this algorithm, each atom is given a "connectivity value" reflecting how many atoms it is connecte

      So you can create as many connection table as possible like the exercise in OLCC website, the correct or "canonical" table is the one that is generated with Morgan algorithm. Is it sound right?