biology

MobiDB

MobiDB is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand MobiDB rather than just read about it. In short: In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured (or disordered) proteins.

Key takeaways

MobiDB belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect MobiDB to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of MobiDB from memory before moving on to harder problems.

Reference excerpt

In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured (or disordered) proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.

MobiDB data sources

Curated data and additional annotation Curated data for MobiDB is obtained from DisProt database giving information and disorder annotation manually extracted from literature. In order to complement disorder annotation, MobiDB features additional annotations from external sources:

UniProt: Annotations from the UniProt database include organism, subcellular location, tissue specificity, function, relevant sites, relevant regions, post-translational modifications, and linear motifs. Pfam: protein domain annotations are displayed in graphical form and are link-enabled, allowing the user to visit the corresponding Pfam page for further information. PDB: Secondary structure is extracted from the PDB whenever available, and displayed in graphical form and in 3D. STRING: Known interactors with evidence in "database" and "experimental" are displayed in a sortable table.

Indirect sources PDB X-ray: When a crystallographic experiment is done to try and resolve a protein's structure, there are cases where the position of certain residues can not be accurately determined. One of the possible causes of this is that the residue is part of a flexible/disordered region. For this reason missing residues in PDB experiments are considered an indication of intrinsic disorder. PDB NMR: Deposited files of NMR experiments for protein structure resolution often contain multiple models, representing different conformations of the same protein. By calculating the differences between the positions of each model's residues, one can measure the degree in which this positions change. This change can be interpreted as a measure of how flexible or disordered a protein is. The MOBI web server (from which the name of this database was derived) automates this calculations taking as input a PDB formatted file.

Predictions A great variety of intrinsic protein disorder predictors have been trained in the last decade. The bulk of them are trained to mimic the nature of the annotations previously described. Since MobiDB currently covers the full set of UniProt sequences, the included predictors need to be extremely fast. Ten predictors currently included (ESpritz in its three flavours, IUPred in its two flavours, DisEMBL in two of its flavours, GlobPlot, VSL2b and JRONN) enable MobiDB to provide disorder annotations for every protein, even when no curated or indirect data is available.

MobiDB consensus In order to provide the best possible annotation for a given protein, MobiDB combines all its data sources into a consensus annotation. This annotation differs from the ones belonging to the sources themselves in that it features a third state, in addition to "structured" and "disordered": when two authoritative sources disagree, it displays the region as "ambiguous". With the currently available annotations, this conflict arises when a manually curated source annotates a certain region as disordered, and yet there is a PDB structure available for that same region.

Website MobiDB website provides users with an interface to search by UniProt ID, protein name or free text. Following the submission, users are presented with a list of proteins each one annotated with disorder information integrated from various sources including consensus disorder prediction. MobiDB web-server exposes some RESTful endpoints allowing programmatic access to MobiDB and retrieval of different data types. Available GET routes provide access to UniProt, STRING, Pfam and disorder data in JSON format.

External links MobiDB homepage

References

Worked examples

Example 1 — a first encounter with MobiDB

Start with the simplest possible case. Write down what MobiDB claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to MobiDB before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about MobiDB ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of MobiDB

In research: MobiDB appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses MobiDB in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: MobiDB is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein databases, so understanding it makes those chapters shorter.
In everyday life: Look for MobiDB outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study MobiDB in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what MobiDB means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain MobiDB out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is MobiDB in simple terms?

Why does MobiDB matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study MobiDB?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on MobiDB.