biology

PDBWiki

PDBWiki 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 PDBWiki rather than just read about it. In short: PDBWiki was a wiki that functioned as a user-contributed database of protein structure annotations, listing all the protein structures available in the Protein Data Bank (PDB). It ran on the MediaWiki wiki application from 2007 to 2013.

Key takeaways

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

Reference excerpt

PDBWiki was a wiki that functioned as a user-contributed database of protein structure annotations, listing all the protein structures available in the Protein Data Bank (PDB). It ran on the MediaWiki wiki application from 2007 to 2013. The website went offline in 2014 and there has not been any way to subsequently access the information that was contributed. PDBWiki contained details of more than 50,000 protein structures and over 50 'user-contributed' annotations, making it a significant resource for the structural biology community.

Motivation The Protein Data Bank (PDB) is the central archive of experimentally solved biomolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.

About PDBWiki was developed as part of the BioWiki initiative, and was entered into the third International Openfree Bioinformation Contents Competition organised by BiO.CC, a biological information website operated by KOBIC. The Website went offline in January 2014, replaced with a notice redirecting to Proteopedia, a similar wiki-based structural biology database project.

See also Molecular and Cellular Biology 'WikiProject'

References

External links The PDBWiki homepage About PDBWiki The Worldwide Protein Data Bank

Worked examples

Example 1 — a first encounter with PDBWiki

Start with the simplest possible case. Write down what PDBWiki 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 PDBWiki 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 PDBWiki 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 PDBWiki

In research: PDBWiki 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 PDBWiki 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: PDBWiki is common in secondary-school and first-year university syllabi. It links to neighbouring topics MediaWiki websites, Protein databases, so understanding it makes those chapters shorter.
In everyday life: Look for PDBWiki 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 PDBWiki in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what PDBWiki 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 PDBWiki out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is PDBWiki in simple terms?

Why does PDBWiki 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 PDBWiki?

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 PDBWiki.