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This button will show the Query page interface. On the Query page itself this button is disabled.
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Some background information about the database BioPath and its retrieval system. The basic statistics about the database shown on this page are retrieved on the fly by counting the records stored in the database tables.
In general there is no need to login to BioPath.Explore, as the publicly accessible version of BioPath.Explore can be used by everybody. However, the following functionality is only available for registered users:
- visualizing the 3D structure within the interactive Jmol applet
- downloading of molecules and reactions as MOL or RXN files
- exporting all structure images of a taxonomy class as PDF file
If you would like to use the full version of BioPath.Explore please feel free to contact Molecular Networks in order to get a quotation of the commercial version of the BioPath system.
Search Bar
Molecules Interface
Basic Search
| Search string | Description |
|---|---|
| molecule name | Search for molecules having given molecule name, e.g., beta-Carotene |
| name/word fragment | Search for molecule names containing given fragment, e.g., glutamate |
| SMILES string | Search for given molecule as full structure and substructure search |
Supported languages: English, Chinese (partly)
The "Autocomplete" functionality is activated on default (e.g., the system shows matching molecule names if more than three characters have been input in the query field).
The SMILES string can be generated by using the JME structure editor.
Structure Based Searches
Start the editor by clicking on the button "Sketch Molecule" and draw your molecule of interest.
After that, click on the "Transfer" button to submit the SMILES string to the input field.
More help about how to use the structure editor will appear after clicking on the "Help" button
within the structure editor window.
The results of the time-consuming substructure searches are cached in the database. Thus, if a user already
requested the same structure search the histlist will be shown within milliseconds instead of several seconds.
Case Sensitive Name Searches
If your search string exactly matches one molecule name the system will return this structure, i.e., if you search for "Glutamate" you will get a detailed page for "L-Glutamate" as "Glutamate" is a trivial name of "L-Glutamate". However, if you are interested all molecules that have "glutamate" as molecule name input "glutamate" (with small letter at the beginning) to receive a list of molecules.
Taxonomy of molecules
For about 90% of the molecules at least one taxonomy entry will be shown on the detail page. This hierarchical classification of molecules is split on the second level into two main categories: "Manual" and "Automatic". The manual taxonomy had been derived by manual inspection of the molecule and assigning a class, whereas the automatic classification is based on a set of defined rules (e.g., substructures, formula).
Advanced Search
| Search string | Description |
|---|---|
| formula=[chem_formula] | Search for molecular formula, e.g., C5H9NO4 |
| weight=[mol_weight] | Search for molecular weight, e.g., weight=147, weight=140:150 (between 140 and 150), weight=:150 (from 0 to 150) |
| complexity=[mol_complexity] | Search for molecular complexity, e.g., complexity=145, complexity=140:160 (range) |
| KEGG=[keggid] | Search for KEGG compound identifier, e.g., KEGG=C00001 or KEGG=None |
| ChEBI=[chebi_id] | Search for ChEBI identifier, e.g., CHEBI=673408 |
| CID=[pubchem_cid] | Search for PubChem identifier, e.g., CID=11840951 |
| id=[mol_id] | Search for structure identifier in BioPath, e.g., id=11415, id=11400:11415 (range), these numbers might change with every update! |
| ubiquitous=[true/false] | Search for molecules that are flagged as being ubiquitous (true) |
Currently, only one advanced search criteria can be performed at a time, i.e., you cannot perform a search on a given formula and molecular weight.
Reactions Interface
Basic Search
| Search string | Description |
|---|---|
| reaction identifier | Search for reactions having given reaction identifier, e.g., RXN00444 or 444 |
| enzyme name | Search for reactions having given enzyme name, e.g., dihydroorotate dehydrogenase |
| name/word fragment | Search for enzyme names containing given fragment, e.g., ligase |
| EC number | Search for reactions having given EC code, e.g., 1.1.1.1 (for alcohol dehydrogenase), 1.2.x.x (for oxidoreductases acting on aldehyde or oxo group as donor) |
Supported languages: English
Advanced Search
| Search string | Description |
|---|---|
| massdifference=[mass difference] | Search for reactions with given mass difference, e.g., massdifference=2 (short: md=2) |
| atomeconomy=[0-1] | Search for reactions with given atom economy, e.g., atomeconomy=0.8:1.0 (from 0.8 to 1.0) or short: ae=0.8:1.0 |
| carbonefficiency=[0-1] | Search for reactions with given carbon efficiency, e.g., carbonefficiency=0.8:1.0 (from 0.8 to 1.0) or short: ce=0.8:1.0 |
| gibbs=[deltaG] | Search for reactions with given range of difference in Gibbs energy [in kcal/mol], e.g., gibbs=5:10 (from 5 to 10), -10:-5 (from -10 to -5) |
Pathways Interface
Pathway Name Search
| Search string | Description |
|---|---|
| pathway name | Search for pathways containing given name, e.g., Biosynthesis of Carotene |
| name/word fragment | Search for pathway names containing given fragment, e.g., Biosynthesis |
Supported languages: English
The "Autocomplete" functionality is activated on default (e.g., the system shows matching pathway names if more than three characters have been input in the query field).
Shortest Path Search
| Search string | Description |
|---|---|
| start/end molecule | Search for the shortest route between two given molecule names as starting and end point |
The shortest path search is based on the Dijkstra algorithm that is performed on a network of molecules (nodes) and reactions (edges).
Reversible reactions are included as forward and backward edges in the network graph.
Molecules flagged as ubiquitous are excluded from the network, otherwise reactions would be linked by such atoms/molecules (protons, water, oxygen, etc.).
Please keep in mind, that the pathway search between two given molecule names cannot be combined with the 'Pathway Name Search'.
Supported languages: English
The "Autocomplete" functionality is activated on default (e.g., the system shows matching molecule names for starting and end point if more than three characters have been input in the query fields).
Result Pages
Molecule Detail Page
Properties calculated from structure
| Property | Description |
|---|---|
| Formula | Molecular formula of the compound |
| Weight | Mass of a compound calculated by using the average mass of each element weighted for its natural isotopic abundance, e.g., carbon atom has an average mass of 12.011 g/mol. unit: g/mol |
| Complexity | Molecular complexity of a compound is a rough estimation how complicated a structure is. |
| XLogP | Estimation of the logP value using the method XLogPv2, as published by R. Wang, Y. Gao and L. Lai (doi:10.1023/A:1008763405023) |
| TPSA | Topological Polar Surface Area as defined by P. Ertl (doi:10.1021/jm000942e) |
| #HDonors | Number of hydrogen donors in a compound. |
| #HAcceptors | Number of hydrogen acceptors in a compound. |
| Gibbs Energy | Prediction of the Standard Gibbs Energy of formation at physiological conditions (pH 7, 25 °C),
as published by M. L. Mavrovouniotis (doi:10.1002/bit.260361013 and JBC). If the value is shown in parenthesis the molecule contains one or more R groups that had been replaced by carbon before calculating the Gibbs Energy. The energies listed for CoA-SH and CoA derivatives are relative values. |
| 1H NMR spectrum | Link to an external webservice that predicts the 1NMR spectrum based on the SPINUS approach published by Aires-de-Sousa (doi:10.1021/ci034228s, doi:10.1021/ci034229k) |
| Isotopic distribution | Link to an external webservice that plots the isotopic distribution graph. |
Structure representations/Cross-references
| Property | Description |
|---|---|
| SMILES | Simplified Molecular Input Line Entry System, more info ... |
| InChI | IUPAC International Chemical Identifier, version 1.02 release 01/10/2009, more info ... |
| InChI-Key | The hashed version of the standard InChI |
| KEGG | Cross-reference to the Kyoto Encyclopedia of Genes and Genomes database |
| ChEBI ID | Cross-reference to the Chemical Entities of Biological Interest database |
| PubChem-CID | Cross-reference to the PubChem database based on identity of InChI keys |
Taxonomy
The taxonomy of molecules is based either on a manual or an automatic derived approach. The automatic method is based on a set of currently about 440 predefined substructures, whereas for the other approach the molecules are annotated manually.
Most similar molecules
The list of most similar molecules is based on an extended version of the 166 MACCS keys published by MDL/Symyx.
Reaction Detail Page
Reaction equation
The reversibility of a reaction is represented by different reaction arrows:
| irreversible reaction |  |
| reversible reaction |  |
| unknown reaction |  |
Reaction conditions
| Property | Description |
|---|---|
| EC number | The Enzyme Commission number for the enzyme catalyzing the reaction |
| Enzyme name | The enzyme name according to the NC-IUBMB |
| Direction | An anabolic reaction builds a compound from smaller units, whereas a catabolic reaction breaks a molecule into smaller parts. |
| Reversibility | The reaction can run in a reversible or irreversible process |
| Oxygen condition | The reaction can run under aerobic or anaerobic conditions |
Properties calculated from reaction
| Property | Description |
|---|---|
| Mass difference | Difference of the sum of the molecular weights of all reactants and the sum of molecular weights of all products |
| Atom economy | Measurement for the conversion efficiency of a chemical reaction, more info ... |
| Carbon efficiency | Amount of carbon atoms in product divided by the total amount of carbon atoms in all reactants, more info ... |
| Gibbs Energy | Prediction of the change in the Standard Gibbs Energy based on Standard Gibbs Energy of formation of reactants and products as published by M. L. Mavrovouniotis (doi:10.1002/bit.260361013 and JBC). |
Cross-references
| Reference | Description |
|---|---|
| Grid square | Grid square the molecule can be found on the Biochemical Pathways wallchart |
| KEGG ID | Cross-reference to the Kyoto Encyclopedia of Genes and Genomes database |
| Rhea ID | Cross-reference to the Annotated reactions database |
| EC->PDB | Cross-reference to the Enzyme Structures Database |
Pathway Detail Page
Network of the pathway
A graph layout of the pathway will be shown if a Adobe Flash plugin is installed.