Molecules Legend

Index:


BioMeta

Returns you to the home page of the BioMeta database.


Molecules

Brings you to the Molecules menu. Is inactive (and shown in red), because you are already there!


Reactions

Brings you to the Reactions menu.


Enzymes

Brings you to the Enzymes menu.


Sources

Brings you to the Sources menu.


Message area

The area were any message is shown (with error messages shown in red and others in blue).


Help

This hyperlink brings you to the clickable map with help texts on all items in the menu (which you are now reading).


Sketch help

Brings you to the help pages (from Molinspiration) of the Java Molecular Editor by Peter Ertl (Novartis).


Sketch pad

The Java Molecular Editor by Peter Ertl (Novartis). It has its separate help facility.


Structure searching

Two forms of structure searching are implemented: whole-molecule and substructure. If the Substructure flag is on, compounds are searched containing the drawn structure as a substructure, otherwise the compounds must match the whole drawn structure.

Whole-molecule searching is implemented through InChI strings. Normally only the main (connectivity) layers (formula, "c", and "h") are used for matching, but stereochemistry ("b", "t", "m", and "s" layers) is also often included. More rarely, isotopes and protonation states ("i", "q", and "p" layers) are included. Currently the fixed hydrogen layers are always excluded for structure matching. See the Unofficial InChI FAQ for details.

Substructure searching is implemented using the FingerPrinter and SDFSubstructureFinder applications from the CDK. The substructure search is conducted in two stages: a pre-screening stage (using FingerPrinter) and an atom-by-atom matching stage (using SDFSubstructureFinder). In the pre-screening stage, a list of features are identified that are present in the query substructure (the so-called fingerprint). This fingerprint is matched, together with the minimum counts of non-hydrogen elements, against the entries in the database resulting in a set of candidate structures. In the atom-by-atom matching stage these candidate structures are matched against the query substructure using a maximum common substructure (MCS) algorithm. This is a computationally expensive operation, hence the pre-screening.

Two flags can be used to control the precision of the structure match: the Stereochemistry flag and the Exact match flag.


Substructure flag

This flag controls whether compounds are searched containing the drawn structure as a substructure, otherwise the compounds must match the whole drawn structure.


Stereochemistry flag

Presently this flag applies only to whole-molecule structure searches and is ignored for substructure searches. It controls whether stereochemistry is taken into account. Stated more precisely, it controls whether the stereochemistry ("b", "t", "m", and "s") layers in an InChI string are used for structure matching. If the flag is on, only the stereoisomer (and if chiral, the enantiomer) exactly as it is drawn will match; if it is off, all stereoisomers (including those with incompletely described stereochemistry) will match (i.e., stereochemistry will be ignored completely). For instance, if the query structure lacks stereochemistry and the Stereochemistry flag is on, the only structures that will match are the ones also lacking stereochemistry. Note also that it is not possible to search for relative stereochemistry (either enantiomer, or the racemate). Try it out for alanine and L-alanine!


Exact match flag

This flag applies only to whole-molecule structure searches and is ignored for substructure searches. It controls whether an exact structure match is required, including isotopes and protonation states. Whole-molecule (as opposed to substructure) searching is implemented through InChI strings. Normally only the connectivity (formula, "c", and "h") and stereochemistry ("b", "t", "m", and "s") layers in an InChI string are used for structure matching. If the Exact match flag is on, additional ("i", "q", and "p") layers are taken into account. These layers involve isotopes, protonation states, and charges. Note that the fixed hydrogen layers are never used. See the Unofficial InChI FAQ for details.


Name

Allows you to search the synonyms of molecule entries, which include common names, systematical names, and (sometimes) trade names. This is a text query option. Note that the Fuzzy match flag determines whether matching is case-sensitive and takes non-alphanumeric characters into account.

When a hit is on display, moving the mouse pointer to the name will allow you to see all the synonyms.


Fuzzy match flag

This flag controls whether non-alphanumeric characters and case are taken into account with name (i.e., synonym) searches. If the flag is off, matching is case-sensitive and performed on all characters; if it is on, matching is incase-sensitive and performed only on alphanumeric characters (i.e., letters and digits).


Systematical name

Allows you to search the systematical names of molecule entries. It is not very useful as a query option because most entries do not have a systematical name. This is a text query option.


#

The database entry number. Included for sake of completeness, but not very useful as a query option unless you know entry numbers (which are not intended for identification of entries, unlike the ID strings). Note that only simple numbers can be used here, no ranges or relational operators.


ID

Allows you to search the ID strings of molecule entries. This is a case-insensitive text query option.


Stereochemistry

The stereochemical information on the displayed compound: "None" if the compound cannot exhibit stereoisomerism; "None (i.e., undefined)" if stereoisomerism is possible but information on stereochemistry is completely absent; "Meso" if the compound has stereocenters but is achiral; "Absolute" if the compound is chiral and the enantiomer shown is the intended one; "Racemic" if the compound is chiral but a racemic mixture is indicated; and finally "Relative" if the compound is chiral but the enantiomer has not been indicated (or the racemic mixture has been intended, note that drugs are often racemates); "Meso", "Absolute", "Racemic", and "Relative" may be followed by the remark "partially defined" if one or more stereocenters are undefined.

The stereochemistry information can be searched using the terms "none", "meso", "absolute", "x" (for racemic!), or "relative" (case-insensitive and only the first character is used for matching).


CAS registry number

Allows you to search the CAS registry numbers of molecule entries. This is a text query option. Since CAS registry numbers don't contain letters, case-sensitiveness is not an issue here.


Internal links

Hyperlink(s) to the "identification data" (full synonym list, InChI, CAS registry number), the 3D structure (if any; generated by Corina), and the reactions (if any) in which the compound is involved. Note that 3D structures are only available for compounds that are stereochemically completely defined and do not contain generic or repeating groups. This field is not searchable.


External links

Hyperlink(s) to the entries from the Compound and Drug sections of the KEGG Ligand database. The actual value for this field is the KEGG Reaction accession number (Cnnnnn or Dnnnnn). This is a case-insensitive text query option.


Element count

The number of different elements in a compound. Not available for compounds containing repeating groups. Note that the generic group "R" counts as an element. This is a integer number query option.

The molecular formula and element count query options can be usefully combined for extensive formula queries.


Molecular formula

The chemical formula of a compound. Not available for compounds containing repeating groups. Note that the generic group "R" may be present in a formula in the same way as any element. In queries, the formula is a list of chemical symbols that each may be followed by a integer number query option, e.g., "C<=10 H10-14 N Cl>2". Note that:

  1. This formula query will only match formulas with just one nitrogen. "At least one nitrogen" would require "N>0".
  2. You cannot ask for the exclusion of particular elements by specifying, e.g., "Br=0" or "Br<1"; this will always result in zero hits.
  3. Attention must be paid to the proper case of the element symbols, or else the element specifications must be separated by spaces. For example, "CO" and "c o" match carbon monoxide, "co" matches cobalt (actually, any compound containing one cobalt atom), and "co2" doesn't match anything (well, it would match any compound containing two cobalt atoms)!

The molecular formula and element count query options can be usefully combined for extensive formula queries.


Molecular weight

The molecular weight of a compound (calculated by taking the natural-abundance mixture of isotopes for each element; c.f. exact mass). Not available for compounds containing generic or repeating groups. This is a real number query option.


Exact mass

The exact mass of a compound (calculated by taking the most abundant isotope for each element; c.f. molecular weight). Not available for compounds containing generic or repeating groups. This is a real number query option.


Search

Submit the query with the query options filled in on the form. All query options are automatically combined in an "and" fashion.


Create

Allows to create a new entry. This option is inactive if you do not have the right to modify the database.


Delete

Allows to delete the current hit. This option is inactive if you do not have the right to modify the database.


Update

Allows to update the current hit. This option is inactive if you do not have the right to modify the database.


Clear

Clears the whole menu and redraws it as an empty input form.


First hit

Brings you to the first hit in the hit set. This option is inactive if the hit set contains just one hit.


Prev hit

Brings you to the previous hit in the hit set. This option is inactive if the hit set contains just one hit.


Next hit

Brings you to the next hit in the hit set. This option is inactive if the hit set contains just one hit.


Last hit

Brings you to the last hit in the hit set. This option is inactive if the hit set contains just one hit.


Goto hit

Brings you to a particular hit in the hit set. This option is active only if you are browsing a hit set with more than three hits. Just type a number in the input field to the right of the "Goto" button, and click on the "Goto" button.


Text query options

Text query options are string searches. They are case-sensitive unless indicated otherwise. Wildcards (using "*") can be used, e.g., "*ucos*phosphate".


Integer number query options

These query options are searches for integer values, allowing comparison and range specifications, e.g., "28", ">=0", "10-19", ">222", and "<=9". Real numbers are not allowed.


Real number query options

These query options are searches for real (floating-point) values, allowing comparison and range specifications, e.g., "3.14159", ">=0.0", "10.51-19.49", ">222.2", and "<=9". Integer numbers are allowed. Note that exponential notation is currently not implemented.