AMBITDatabase HELP

How to process current structure (last revision - 14 June 2007)

By default, all the actions below are applied to the currently (displayed) molecule in Molecule browser. Current molecule can be changed by browsing the data set by navigation bar in Molecule browser.

This behaviour can be changed so that the actions apply to all molecules in the browser. For this purpose, consult Molecule processing options in   Search options.

  1. Generate 3D coordinates from structure (by CDK 3D builder);
  2. consult AQUIRE data. Select the AQUIRE tab at the bottom to observe the data. 
  3. generate metabolites. Only limited number of hydrolysis reactions are implemented;
  4. calculate descriptors available;
  5. mark the current data set in the database so it can be further accessed by name (Save as dataset);
  6. use the built-in structure diagram editor to alter an existing substance or to input a new one from scratch;
  7. get Mode of Action classification by Verhaar scheme;
  8. estimate toxicity class Cramer scheme;
  9. estimate skin irritation and corrosion potential by BfR rules;
  10. observe and edit the corresponding 2D structure by JChemPaintstructure diagram editor;
  11. retrieve other information from database
  12. calculate electronic parameters. This invokes WinMopac and may take a while for large molecules;
In adition, you can:
  1. save the current data set in a file (compatible file types include SDF, MOL, CSV, TXT, CML, HIN, PDB, SMI, XYZ, SVG) by File/Save menu;
  2. open a file with substances (compatible file types include CSV, TXT, SDF, MOL, MOL2, SMI, CML, HIN, ICHI, INCHI, PDB, XYZ) by File/Open menu;
  3. browse the file contents through the links at the bottom of the structure diagram;
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Developed (2006,2007) by Joanna Jaworska and Nina Jeliazkova for CEFIC-LRI