Frequently Asked Questions FAQ

About MuteinDB

About querying muteinDB

About the search results

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.
The muteinDB contains experimentally derived data about muteins from publicly available sources as well as data directly submitted by scientists.
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.
All basic information about underlying wild type protein sequences, structures and origin as well as compound structures and the respective references are retrieved from publicly available databases (PubMed, PubChem, UniProt, PDB,....) and are linked to the corresponding databases.
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 ( download this file ) the guidelines for collecting data in the MS Excel file can be downloaded here ( download this file ). 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.

MuteinDB Schema
Fig. 1 Schematic diagram of MuteinDB Structure
Using this basic search, users can search for a substrate of interest by entering the substrate name or CAS Number in the text field.
Basic search by substrate (home screen)
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.
Left side navigation menu Search by Reaction
Fig. 3 menu of "Search by Reaction".
The query interface offers several parameters, of which one or several can be used.
  • Substrate/product: A specific substrate/product of choice can be used to search for all the related enzymes present in the database (e.g. testosterone). Queries can be typed in the text box, as full name or CAS number as well as starred abbreviation (wildcard) for multiple hits. While tipping a suggest box appears where substrate can be chosen from.
  • Reaction type:Wild type or mutant enzymes capable of performing various reaction types can be searched within MuteinDB. Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
  • EC Number:Entering the Enzyme Commission number allows to limit the search to a certain enzyme class. Queries can be typed in the text box. While tipping a suggest box appears where appears where entries can be chosen from
  • Wild Type: Specifying an underlying wild type enzyme limits the search to muteins derived of this wild type (e.g. CYP102A1). Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
  • Organism: Search can be limited to a specific source organism (e.g. Bacillus megaterium). Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
  • Tissue: If available, the search can be limited to a specific tissue localization for every enzyme present in the database. Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
To narrow the results, parameters can be added or excluded.
Search by Reaction interface
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
JME interface of Search by Structure
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.
Search by Structure result list
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.
Left side navigation menu Search by Inhibitor
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".
Search interface of Search by Mutation
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.
Left side navigation Search by Mutation
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".
Search interface of Search by Mutation
Fig. 10 Search interface of "Search by Mutation".
All available reactions of muteins containing the selected mutations are shown as a result list.
In this section users can search for a specific mutant enzyme (mutein).
Left side navigation Search by Mutein
Fig. 11 menu of "Search Mutein"
Search interface of Search by Mutein
Fig. 12 Search interface of "Search Mutein".
The following parameters can be individually searched:
  • Mutein name: A specific mutant version of the enzyme of interest can be searched (e.g. CYP102A1-F88A). Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
  • Wild Type: Muteins of the underlying wild type version of the enzyme of interest can be searched (e.g. CYP102A1). Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from. A specific search by wild type enzyme is available as a separate search option.
Left side navigation menu Search by Wild Type
Fig. 13 Left side navigation menu.
  • Substrate: A specific substrate of choice can be entered (e.g. testosterone). Queries can be typed in the text box, as full name or CAS number as well as starred abbreviation (wildcard) for multiple hits. While tipping a suggest box appears where substrate can be chosen from.
  • EC Number:Entering the Enzyme Commission number allows to limit the search to a certain enzyme class. Queries can be typed in the text box. While tipping a suggest box appears where appears where entries can be chosen from.
  • Organism: Search can be limited to a specific source organism (e.g. Bacillus megaterium). Queries can be typed in the text box, as full names as full names as well as starred abbreviation (wildcard) for multiple hits. While tipping a suggest box appears where entries can be chosen from.
  • Tissue: If available, the search can be limited to a specific tissue localization for every enzyme present in the database. Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
  • Expression Host: Specific hosts for heterologous expression of enzymes present in the database can be searched. Queries can be typed in the text box. While tipping a suggest box appears where entries can be chosen from.
To narrow the results, parameters can be added or excluded.

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:
General Result View
Fig. 14 General Result view.
Clicking on Edit Display Settings, on the upper right corner, a selection mask will appear:
Display setting preferences of the default result page.
Fig. 15 Display setting preferences of the default result page.
Selection mask of Display settings option
Fig. 16 Selection mask of Display settings option.
The ticked parameters will be shown in the query.
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.
Refine display settings
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:
Refine display settings
Fig. 18 side-by-side comparison of muteins.

All mutein names are linked to the more detailed "mutein view".
Examples for linked mutein names
Fig. 19 Examples for linked mutein names.
substrate section of the general mutein view
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
Sequence section of the general mutein view
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"