BiSSCat Help[Help page HOME] [Show all]
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). The text-search option is located at the top of the homepage and can be used to search for:
- any term for compounds, functional groups, substructures and enzymes,
- molecular formulae of compounds, functional groups or substructures
- EC numbers and other IDs registered in BiSSCat.
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.
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. The SUBSTRUCTURE database was constructed using data on the structures of 10,046 and 247,617 chemical compounds derived from the KEGG and NCI databases, respectively, in MDL Molfile format. For convenience, the original database IDs assigned to compounds have not been changed, so that they can be used to link to the corresponding data in the source databases.
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. FGROUP is an index of functional groups and substructures. Each FGROUP entry has one or more names, which helps one look up corresponding compounds or substructures. See F311100 Primary Alcohol as an example.
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.
The Multiple Substructure Search enables one to search compounds by including or excluding FGROUP or SUBSTRUCTURE entries. Step 1: Cookies have to be enabled.
Step 2: The Multiple Substructure Search page is seen by clicking "Multiple" in the menu (1). If no FGROUP or SUBSTRUCTURE entry has been looked up in your computer, the list of recently searched entry is empty as shown in the picture below.
Step 3: After FGROUP or SUBSTRUCTURE entries are searched (2,3), they are added to the list of recently searched entry (4).
Step 4: More FGROUP or SUBSTRUCTURE entries can be added to the list in the same ways (5-7). Data of recently searched items are stored in your computer as cookies, which will expire automatically in 7 days.
Step 5: Check Include or Exclude the recently searched items (8) and press Submit (9), then the Multiple Substructure Search will be performed. You do not necessarily check all items; the only items that are checked will take effect in the search. It may take several minutes, so please wait until the total result is shown.
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.
SUBSTRUCTURE is a collection of pre-calculated chemical substructures (See S0000137 as an example), which have been derived from these different aspects below:
- 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
- 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
- Donor of hydrogen bond
- Acceptor of hydrogen bond
- Polar (can be either a donor or acceptor of a hydrogen bond)
- Other properties:
- Nitrogen of an amide group
- Carbon of a carboxylate group
- Conjugated double bonds
- 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
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. Here are the ATOM entries for C, O, N, S and P, that have the most numbers in this database:
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. Examples: