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The outcomes of processes on our target databases (BMRB, PubChem, HMDB, PDB RCSB Ligand-Exp) are shown in this tab.

  1. Correct and complete molecule and atom identifiers of entries of the target databases:
  2. You can query a rigistry ID of the processed databases and see ALATIS results. If you need the complete set of the processed data of any of our target databases, please contact Hesam Dashti (dashti@wisc.edu).

    The search term is prefilled by the PubChem ID 3362, you can try one of BMRB ID's (e.g. write bmse000001), HMDB ID's (e.g. write HMDB00002), or PDB RCSB Ligand-Exp ID's (e.g. write 0AL).



         
         



  3. Flagged improper usage of InChI strings in databases:
    1. Incorrect/incomplete InChI strings deposited in databases:
      1. This section lists the inconsistencies between standard InChI that we generated and those deposited in databases:
      2. BMRB list can be found here.
        HMDB list can be found here.
        PubChem list can be found here.
        PDB list can be found here.

      3. This section lists the inconsistencies between standard InChI that we generated and those deposited in databases, after discarding the standard falg of InChI strings:
      4. BMRB list can be found here.
        HMDB list can be found here.
        PubChem list can be found here.
        PDB list can be found here.

    2. Flagged deposited cross-links from BMRB and HMDB entries to PubChem:
    3. For every cross-link in the BMRB and HMDB entries to the PubChem entries, we compared their standard InChI strings and flagged the corss-links that their corresponding molecule identifiers do not match:
      Flagged cross-links in BMRB can be found here.
      Flagged cross-links in HMDB can be found here.

  4. Created cross-links from PDB entries to BMRB, HMDB, and PubChem entries:
  5. We used the standard molecule identifiers of PDB entries and compared them with the corresponding identifiers of BMRB, HMDB, and PunChem entries. Here are the results of created cross-links:
    Created cross-links to BMRB can be found here.
    Created cross-links to HMDB can be found here.
    Created cross-links to PubChem can be found here.

  6. Incompatible atom labels between BMRB and HMDB
  7. Comparing deposited atom labels of entries of the same compounds can be found here

Citation:
  • Hesam Dashti, William M. Westler, John L. Markley, Hamid R. Eghbalnia, "Unique identifiers for small molecules enable rigorous labeling of their atoms", in press Nat. Sci. Data, 2017.
Disclaimer:
  • ALATIS is available to the public as a web-service via our web-server, and also through the NMRBox virtual machine. The custom source code, developed using the academic license of MATLAB® in the Linux environment (MATLAB® 2016a for CentOS 6.5). This work is copyrighted under the terms of GPL. The web-service and the source codes are provided on an “as is” basis without warranty of any kind, either expressed or implied. Any usage of the web-server, or modification and application of the source codes are free for academic use when ALATIS publication is cited.
  • The input/output file formats to ALATIS are Mol V2000 and its corresponding SDF. Other acceptable input/output file formats of this website are provided by utilizing the academic version of ChemAxon software package, meaning this web-server is only for non-commercial research or educational purposes. When you use these additional file formats, please also acknowledge ChemAxon by including:"Marvin was used for drawing, displaying and characterizing chemical structures, substructures and reactions, Marvin 16.7.11, 2016, ChemAxon (http://www.chemaxon.com)". Marvin acknowledgement was extracted from here on March 2017.
Contact:
    For any question or concern please contact Hesam Dashti (dashti@wisc.edu).
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