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BiSSCat Help

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How to use the help page

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).

BiSSCat Objects

ObjectExplanationExample
FGROUP Index of functional groups and substructures F311100 Primary Alcohol
SUBSTRUCTURE Collection of pre-calculated chemical substructures S0000137
COMPOUND Chemical compound information derived from KEGG and NCI databasesC00005 NADPH
ENZYME IUBMB Enzyme ListEC 1.4.3.4

Text-search options

The text-search option is located at the top of the homepage and can be used to search for:
  1. any term for compounds, functional groups, substructures and enzymes,
  2. molecular formulae of compounds, functional groups or substructures
  3. 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.

Examples:

Searching COMPOUND

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.

MethodExplanationDetail
Text search Looking up compounds by name or ID (Help)
Tree search Hierarchical classification tree based on structure or activity
Structure search based on elements, electrostatic and physicochemical properties (Help)
Multiple Substructure Search search compounds by including or excluding FGROUPs (or SUBSTRUCTUREs) (Help)

Data source

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.

Searching ENZYME

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.

MethodExplanationDetail
Text search Use to look up enzymes by name or EC number (Help)
Tree search Use to view the Enzyme List arranged by class, subclass and sub-subclass, i.e. hierarchically
Structure search

Use to search by reaction equation (either full or partial), as well as by substructure or by compound(s) found in enzyme reactions

Examples:

What is FGROUP?

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.

Searching FGROUP

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.

MethodExplanationDetail
Text search Looking up FGROUPs by name or ID (Help)
Tree search Hierarchical classification tree based on elements and topology
Structure search based on elements, electrostatic and physicochemical properties (Help)

Multiple Substructure Search

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

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.

What is SUBSTRUCTURE?

SUBSTRUCTURE is a collection of pre-calculated chemical substructures (See S0000137 as an example), which have been derived from these different aspects below:

What is ATOM?

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:

What is BOND?

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:

What is CONJ?

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.

Examples:

What is FRAG?

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.

Examples:

What is RING?

A RING entry is a cyclic substructure, one of the pre-calculated SUBSTRUCTURE types. RING entries can be searched using Substructure Search option.

Examples:

What is SKEL?

SKEL is a carbon skeleton, one of the pre-calculated SUBSTRUCTURE types. SKEL entries can be searched using Substructure Search option.

Examples:

What is VICI?

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.

Examples:

Searching SUBSTRUCTURE

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:

MethodExplanationDetail
Text search Looking up SUBSTRUCTUREs by ID (Help)
Structure search based on elements, electrostatic and physicochemical properties (Help)

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.

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."


SVG images

Each chemical compound entry has an automatically generated interactive SVG image, which can be used to find the substructure of interest.


BiSSCat v1.07.31 http://bisscat.org/
Developed by Masaaki Kotera, Department of Biochemistry, Trinity College Dublin.
Science Foundation of Ireland is gratefully acknowledged.