Frequently Asked Questions FAQ
About MuteinDB
- Why muteinDB?
- What kind of information can I find in muteinDB?
- Who maintains muteinDB?
- How can I support muteinDB with new data?
About querying muteinDB
- Simple search by Substrate (home screen)
- How to search by Reaction
- How to search by Structure
- How to search by Inhibitor
- How to search by Mutation
- How to search by Mutein
About the search results
- How is the relative activity defined?
- How to change the display settings of the search results?
- How can I compare two or more muteins of interest?
- How can i get to the detailed information of muteins after a successful search?
- Are there information linked to external resources (e.g. PubMed)?
muteinDB tutorials
Information about certain proteins
and their muteins are widely spread in literature. The growing interest
of the pharmacology and medical scientists in individualized medicine
and the increasing interest in tailor made enzymes for the fast growing
biocatalysis industry lead to an exponential increase of literature
about muteins and their influence on the enzymes’ kinetic properties.
Presently, the understanding of the structure-function relationship of proteins is still limited. It is, therefore, of broad interest to keep as much data as possible in a simple and easy-to-use manner.
MuteinDB is a comprehensive and systematically compiled database of muteins and their kinetic data of catalyzed reactions (including inhibition), but also facilitates the easy and efficient search through the data and the presentation of the results in a convenient, clear manner.
Presently, the understanding of the structure-function relationship of proteins is still limited. It is, therefore, of broad interest to keep as much data as possible in a simple and easy-to-use manner.
MuteinDB is a comprehensive and systematically compiled database of muteins and their kinetic data of catalyzed reactions (including inhibition), but also facilitates the easy and efficient search through the data and the presentation of the results in a convenient, clear manner.
The muteinDB contains experimentally
derived data about muteins from publicly available sources as well as
data directly submitted by scientists.
The collected data include:
The collected data include:
- information about muteins and their catalyzed reactions (substrates, products, reaction type, ...) including kinetic data (activity, Km, kinetic resolutions).
- information about inhibitors are stored (inhibitor, Ki,...)
- conditions used for data generation (Buffer, Temperature, Solvents,....)
- information about substrates, products and inhibitors include the CAS or a CID number as a unique identifier.
- furthermore, the expression host, employed co-factors and co-proteins are included.
The collection of data sets was done
and will be continued within the EU FP7 project OXYGREEN (http://www.OXYGREEN.org). To ensure
continuation of data collection and curation of the database, MuteinDB
was furthermore integrated into several other currently financed
projects. Other scientists are encouraged to provide data for other new
or already existing muteins. For contact information see
"contact".
To simplify and facilitate updating
and incorporation of new data, an import procedure is integrated in the
database. Therefore, all relevant data for the MuteinDB are collected in
an excel sheet according to standardized guidelines.
Scientists can download the MS Excel import template here (
) the guidelines for collecting data in the MS Excel file can be downloaded here (
). The MS Excel file containing the collected data can then be sent to one of our scientists responsible for database curation. (see
"contact")
During data import, the MS Excel files are checked for consistency according to the guidelines and compared to the already existing mutein data to prevent double entries. If some inconsistencies occur an error report is generated and will be sent back together with the provided MS Excel file for revision. Only a few selected scientists are allowed to update and integrate data directly into the database, this precaution ensures the consistency and integrity of the data contained in the MuteinDB.
Scientists can download the MS Excel import template here (


During data import, the MS Excel files are checked for consistency according to the guidelines and compared to the already existing mutein data to prevent double entries. If some inconsistencies occur an error report is generated and will be sent back together with the provided MS Excel file for revision. Only a few selected scientists are allowed to update and integrate data directly into the database, this precaution ensures the consistency and integrity of the data contained in the MuteinDB.
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Fig. 1 Schematic diagram of MuteinDB Structure |
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Fig. 2 Basic search by substrate (home screen). |
In this section, users can search for a reaction of interest by entering product and or substrate. |
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Fig. 3 menu of "Search by Reaction". |
The query interface offers several parameters, of which one or several can be used. |
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Fig 4. Search interface of "Search by Reaction". |
Molecular structures can be searched within MuteinDB. A Java module is loaded, and a user-friendly interface allows drawing and submitting a desired structure to be searched within MuteinDB
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Fig. 5 JME interface of "Search by Structure". |
Once the desired structure is drawn (1), press the Search Molecule button (2), and a list of possible substrates or inhibitors will appear on screen. |
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Fig. 6 "Search by Structure" result list. |
After selection of the desired target(s) and the target molecule type the MuteinDB will be enquired. |
In this section, users can search for inhibitors for a specific wild type or mutant enzyme.
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Fig. 7 Left side navigation menu. |
Queries can be typed in the text box next to the "Inhibitor" label, as full name or CAS number as well as starred abbreviation (wildcard) for multiple hits. While tipping a suggest box appears where inhibitor can be chosen from. A refined search, selecting an inhibitor against a specific mutein or wild type enzyme can be performed, selecting the desired enzyme in the boxes corresponding to "Mutein name" or "Wild Type". |
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Fig. 8 Search by Inhibitor interface. |
To narrow the results additional parameters can be added or excluded. |
In this section users can search for muteins containing a certain mutation. |
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Fig. 9 Left side navigation menu. |
Specifying an underlying wild type enzyme limits the search to muteins derived of this wild type (e.g. CYP2D6). Queries can be typed in the text box, as full names as well as starred abbreviation (wildcard) for multiple hits. While tipping a suggest box appears where entries can be chosen from. One or several Positions can be entered in the text filed next to the "Position" lable (e.g. 120, 254). Original and modified amino acids can be selected. Multiple selections are possible by "control" + "mouse click". |
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Fig. 10 Search interface of "Search by Mutation". |
In this section users can search for a specific mutant enzyme (mutein). |
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Fig. 11 menu of "Search Mutein" |
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Fig. 12 Search interface of "Search Mutein". |
The following parameters can be individually searched:
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Fig. 13 Left side navigation menu. |
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The relative activity is calculated with reference to the kinetic data of the wild type reported together with the mutein of the same literature source.
% > → mutein is more active than the wild type.% > → mutein is less active than the wild type.
Display setting preferences can be
adjusted directly from the result page.
Upon submitting any enquiry in MuteinDB, a page like the following will appear:
The ticked parameters will be shown in the query.
Upon submitting any enquiry in MuteinDB, a page like the following will appear:
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Fig. 14 General Result view. |
Clicking on Edit Display Settings, on the upper
right corner, a selection mask will appear: |
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Fig. 15 Display setting preferences of the default result page. |
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Fig. 16 Selection mask of Display settings option. |
Any mutein, obtained after searching according to any parameter, can be side-by-side compared upon clicking in the tick box next to the mutein of interest: The following fig. 17 shows a snippet of the result screen. The check box where to select muteins for comparison is highlighted.
Upon ticking the boxes, a side-by-side comparative table will be shown, fig. 18:
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Fig. 17 Search result screen snippet, with highlighted compare box. |
Upon ticking the boxes, a side-by-side comparative table will be shown, fig. 18:
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Fig. 18 side-by-side comparison of muteins. |
All mutein names are linked to the more detailed "mutein view".
The mutein view shows detailed information.
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Fig. 19 Examples for linked mutein names. |
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Fig. 20 "Substrate section" of the general "mutein view" |
The mutein view shows detailed information.
- Basic DataShows basic information about name, origin, UniProt ID, GenBank ID etc. as well as information about the data entry creation.
- PropertiesShows basic information about name, origin, UniProt ID, GenBank ID etc. as well as information about the data entry creation
- SubstrateDetailed information about catalyzed reactions are given. This includes kinetic data as well as expression host, co-protein and used co-factors. Additionally information about the reference is given.
- SequenceSide-by-side comparison of the wild type and the mutein sequence is shown. Positions with known mutations are highlighted and are linked to the "Enzyme Mutation View" where all mutants containing a mutation at the selected position are shown. Additionally the amino acid sequence of the mutein can be downloaded as FASTA file
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Fig. 21 Sequence section of the general mutein view. |
Several information is linked to external databases.
- PubMedID → linked to the PubMed entry.
- Substrate / Product and Inhibitor names → linked to the PubChem entry.
- EC Number → linked to the BRENDA entry.
- GenBankID → linked to the GenBank entry.
- UniProtID → linked to the UniProt entry.
- PDB → linked to the PDB entry
- Organism → linked to the “Taxonomy Browser” entry
Tutorial 1 With this tutorial we want to show you first steps in how to use the MuteinDB. |
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Tut. 1 Getting started with MuteinDB. |
Tutorial 2 With this tutorial we want to show you how one can customize the apperance of the search result list |
Tut 2. MuteinDB tutorial 2. Customize the result list |
Tutorial 3 With this tutorial we want to indroduce you to the compare function of the MuteinDB |
MuteinDB tutorial 3. Compare function. |
Tutorial 4 With this tutorial we want to show you where you can find detailed information about the muteins |
MuteinDB tutorial 4. Detaild information. |
Tutorial 5 With this tutorial we want to show you an example how to retrive more focused data sets by using the "Search by Reaction" querying option. |
MuteinDB tutorial 5. "Search by Reaction" |
Tutorial 6 With this tutorial we want to show you how the exciting feature "search by structure" works. |
MuteinDB tutorial 6. "Search by Structure" |
Tutorial 7 With this tutorial we want to show you how to browse catalyzed reactions of |
MuteinDB tutorial 7. "Search by Mutation" |