Using FuzDB The core of FuzDB is the Browse module. Data in the Table of Entries provides basic information about the assembly, including the specification of the partners and the annotation of the fuzzy region(s). All fuzzy complexes have an identifier in the format of FCxxxx, and the same protein can be involved in multiple entries. The protein name also includes domain specifications and abbreviations.
Upon clicking on the FC ID or the Protein name you can get to the expanded entry page. Expanded entry page
Only those fields are displayed, where relevant information is available. Search Simple text search The simple text surveys all sections of the Table of Entries and the Expanded Entry. Unlike the advanced search it cannot be limited to specific columns or fields. This option is useful for example to list fuzzy complexes with specific functions or from a set of species (e.g. yeasts). A simple text search is an efficient way to look for expressions that are located in the descriptive sections of the Expanded Entry page. For example, applying the “unfolding” filter will select proteins that unfold or expand upon binding to their partners. to find entries in the database. Advanced search The advanced search option is to look for terms in specific sections, such as protein or partner name, the PDB or BMRB code, or PubMed ID. The user may also search for fuzzy complexes which have been determined by a given experimental technique, as listed in the Methods module. It is possible to use a combination of specific fields, such as topology and mechanism. For example, applying “flanking” (topology) and “tethering” (mechanism) filters will select those fuzzy regions which flank ordered binding sites and serve to anchor them to their partners. Both searches are case insensitive. The results could be downloaded in text format using Text view option in the menu. Methods The Methods module collects the experimental techniques, which have been applied to study fuzzy assemblies. Methods is linked to the Detection method column of the Table of Entries in the Browse module and can also appear as a pop-up window. Classes The Classes module describes the topological and mechanistic categories of fuzzy complexes. This is linked to the Class column of the Table of Entries in the Browse module and can also appear as a pop-up window. Upload The Upload module is for submission of new entries to the database. This module is highly protected, with the user requiring a safety key to upload data, which can be obtained by email. The process of submission is described in detail step-by-step and the data will be validated. By providing an email address, the user receives an electronic code that enables him/her to submit data. The required fields are the name of the protein and partner(s) and either the structural or the biochemical evidence, although for a new FuzDB entry both types of data will be required. The user is advised to provide a reference, such as a PubMed or a structure identifier. Specifying the sequence of the protein is recommended, but is not obligatory. An automatic email is generated upon submission to notify the FuzDB team. In most cases, the authors are contacted for missing or ambiguous information and an extensive literature search is performed to complement data. Obviously, email inquiries regarding fuzzy complex candidates are also considered. The contact name and email of the submitter is displayed in the Expended Entry page. Analysis The Analysis module provides examples for analysis and interpretation of data for individual systems and for comparative analysis of fuzzy complexes.
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