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
C6O6
Each chemical compound entry has an automatically generated interactive SVG image, which can be used to find the substructure of interest.
A RING entry is a cyclic substructure, one of the pre-calculated SUBSTRUCTURE types. RING entries can be searched using Substructure Search option.
One can use the text-search option to search the whole of BiSSCat or one can limit the search to compound, FGROUP, enzyme, reaction or SUBSTRUCTURE by selecting the item of interest from the drop-down menu. There are also alphabetically ordered lists of all FGROUPs, compounds and enzymes.
Examples:
Each ENZYME entry has an EC number and one or more names, which can be searched using the Text-search option. Other search options are described below. To begin the search, click on the hyperlink describing the type of search you want to perform.
Use to search by reaction equation (either full or partial), as well as by substructure or by compound(s) found in enzyme reactions
The Multiple Substructure Search enables one to search compounds by including or excluding FGROUP or SUBSTRUCTURE entries.
SKEL is a carbon skeleton, one of the pre-calculated SUBSTRUCTURE types. SKEL entries can be searched using Substructure Search option.
VICI is one of the pre-calculated SUBSTRUCTURE types. VICI entries are defined in terms of ATOM entries, i.e., a central atom and the atoms attached to it. VICI entries can be searched using Substructure Search option.
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.
Click 'Help' (1), then the help page will be seen. The 'Help' box is white while you are looking at the help page. Click '[Show all]' in the help page (2) in order to see all contents of the help page.
You will find the corresponding help page whenever you click the 'Help' box. For example, click 'FGROUP' (3) and click 'Help' (4), you will see the help page for FGROUP. Clicking the 'Help' box while seeing the help page leads one to the top of the help page. Clicking one of the other boxes while seeing the help page leads one to the corresponding page (not the help page) (5).
ATOM is one of the pre-calculated SUBSTRUCTURE types. ATOM entries are distinguished by their elements and by their electrostatic and physicochemical properties, which are calculated for each non-hydrogen atom of each compound. Hydrogen atoms are not assigned individual ATOM entries, but are included with their adjacent non-hydrogen atoms. ATOM entries can be searched using Substructure Search option.
A FRAG is one of the pre-calculated SUBSTRUCTURE types, and is defined as a fragment obtained when all rotatable bonds are cut. A rotatable bond is defined in the following way: only a single bond (saturated bond) that is not included in any ring substructure can be rotated. Amide bonds are not rotatable as they are known to have an energy barrier that prevents rotation. Two cases that have not yet been considered are where steric hindrance prevents rotation, and where an enzymic reaction helps rotation (such as occurs with cis-trans-isomerases). A bond consisting of one hydrogen atom and one non-hydrogen atom is also excluded. FRAG entries can be searched using Substructure Search option.
A CONJ entry is consisting of conjugated double bonds, one of the pre-calculated SUBSTRUCTURE types. CONJ entries can be searched using Substructure Search option.
BOND is a chemical bond consisting of two non-hydrogen atoms, one of the pre-calculated SUBSTRUCTURE types. BOND entries can be found using Substructure 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.
Each FGROUP entry has an ID number and one or more names, which can be searched using the Text-search option. Other search options are described below. To begin the search, click on the hyperlink describing the type of search you want to perform.
Each COMPOUND entry has an ID number and one or more names, which can be searched using the Text-search option. Other search options are described below. To begin the search, click on the hyperlink describing the type of search you want to perform.
All SUBSTRUCTURE entries have ID numbers to be looked up by Text-search option. Some of them have links to FGROUP entries, by which SUBSTRUCTURE entries can be found. There is another option to look up SUBSTRUCTURE entries:
