Search by Structure

• BiSSCat Structure Search option
• Physicochemical and Electrochemical Properties
• Examples: Elements and Database
• An example of searching steps
• Click here to see all contents in the help page.

BiSSCat Structure Search option

The BiSSCat Structure Search option can be used to look up compounds, functional groups, and substructures based on structural information or physicochemical properties.

• Elements: This option is used to specify the elements comprising functional groups or substructures (e.g. CO2 for carboxylate, C6O6 for sugars, etc). The number of hydrogen atoms is not taken into account unless specified explicitly.
• The database is divided into a number of subsections based on the type of data, as follows:
  • compound
  • fgroup: an index of functional groups and substructures
  • substructure: a collection of pre-calculated substructures
    • atom: an atom with physicochemical/electrochemical properties
    • vici: a central non-hydrogen atom and the atoms attached to it
    • bond: a chemical bond consisting of two non-hydrogen atoms
    • ring: a cyclic substructure
    • frag: a fragment obtained when all rotatable bonds are cut
    • skel: a carbon skeleton/backbone
    • conj: conjugated double bonds
• Properties: physicochemical and electrochemical properties

Physicochemical and Electrochemical Properties

Physicochemical and electrochemical properties are defined in each ATOM entry, and can be used in the BiSSCat Structure Search option. Most of these properties (excluding ring properties) are based on the programmable atom typer program, PATTY (Bush and Sheridan, 1993).

Note that the physicochemical properties are provided for each non-hydrogen atom (ATOM entry) rather than for the total structure of the chemical compound. For example, while ethanol (CH3CH2OH) is a hydrophilic molecule, using the PATTY method, the two carbon atoms of the ethyl group (CH3CH2-) and the oxygen atom of the hydroxy group (-OH) are assigned as being "hydrophobic" and "polar", respectively.

• Orbital:
  • sp
  • sp2
  • sp3
• Ring:
  • 3-membered ring
  • 4-membered ring
  • 5-membered ring
  • 6-membered ring
• Aromatic ring:
  • 3-membered aromatic ring
  • 4-membered aromatic ring
  • 5-membered aromatic ring
  • 6-membered aromatic ring
• Topology:
  • Attached to 0 non-hydrogen atoms
  • Attached to 1 non-hydrogen atom
  • Attached to 2 non-hydrogen atoms
  • Attached to 3 non-hydrogen atoms
  • Attached to 4 non-hydrogen atoms
• Electrochemical properties: under physiological conditions
  • Cation
  • Anion
  • Donor of hydrogen bond
  • Acceptor of hydrogen bond
  • Polar (can be either a donor or acceptor of a hydrogen bond)
  • Hydrophobic
  • None
• Other properties:
  • Nitrogen of an amide group
  • Carbon of a carboxylate group
  • Conjugated double bonds
  • Resonance

Examples: Elements and Database

The (sub)structure search option works when both the elements (or molecular formulae) and the database are specified. Number of hydrogen atoms can be specified. Otherwise it is ignored.

CO2

in compound	in fgroup	in substructure

C6O6

in compound	in fgroup	in substructure

An example of searching steps

1. C6
   When no database is specified, corresponding compounds are searched.
   
   
   
2. In substructure
   Database is specified.
   
   
   
3. Excluding ring
   Check Exclude, select RING and Submit, then substructures consisting of C6 without 3-, 4-, 5- or 6-membered cyclic structures are obtained.
   
   
   
4. Including sp2
   Select sp2 and Submit, then substructures consisting of C6 without cyclic structures including one or more sp2 atoms are obtained.
   
   
   
5. Including 4 sp2 atoms
   The number of sp2 atoms can be specified. Select 4 and Submit, then substructures consisting of C6 without cyclic structures including 4 sp2 atoms are obtained. (The figure in brackets indicates the number of substructures that correspond to the search criteria.)
   
   
   
6. Including aromatic ring
   By adding this criterion to the search terms, the number of corresponding substructures will be reduced to zero. In this case, the last query will be ignored in a subsequent search.
   
   
   
7. Including ring
   The query had been "excluding ring", but the last query is "including ring". In this case, the last query is prioritized.
   
   
   
8. Reset sp2
   The query had been "Including 4 sp2 atoms". By clicking on Reset, selecting sp2 and pressing Submit, the sp2 element of the search is cancelled.
   
   
   
9. Including 5-membered aromatic ring
   Select 5-membered aromatic ring and Submit.
   
   
   
10. Including 6-membered aromatic ring, and 2 atoms are part of 5-membered aromatic ring
    Two different queries "Including 6-membered aromatic ring" and "2 atoms are part of 5-membered aromatic ring" can be processed simultaneously.
    
    
    
11. 6 atoms are part of 6-membered aromatic ring
    The final query becomes "Search substructures consisting of C6, 2 and 6 of which is part of 5-membered and 6-membered aromatic ring, respectively."