biology

PDBbind database

PDBbind database 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 PDBbind database rather than just read about it. In short: The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB). It thus provides a link between energetic and structural information of protein-ligand complexes, which is of great value to various studies on molecular recognition occurred in biological systems.

Key takeaways

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

Reference excerpt

The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB). It thus provides a link between energetic and structural information of protein-ligand complexes, which is of great value to various studies on molecular recognition occurred in biological systems.

History The aim of the PDBbind database is to provide a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). It thus provides a linkage between energetic and structural information of these complexes, which may be used for various studies on molecular recognition occurred in biological systems. The PDBbind database was first released to the public in May, 2004.

Current release The PDBbind database is updated on an annual basis to keep up with the growth of the Protein Data Bank. The current release, i.e. version 2014, is based on the contents of Protein Data Bank released on Jan 1st, 2014. This release provides two basic types of information:

Basic information of ~13000 complex structures formed between protein-small molecule ligand, protein-protein, protein-nucleic acid and nucleic acid-small molecule ligand. The user can display and examine these complex structures on-line. The user can also search through the chemical structures of the ligand molecules included in these complexes. Binding affinity data and structural information for a total of 12,995 biomolecular complexes, including protein-ligand (10656), nucleic acid-ligand (87), protein-nucleic acid (660), and protein-protein complexes (1592), which is the largest collection of this kind so far. Binding data included in version 2014 have increased by 20% as compared to version 2013. All of these data are collected from >28,000 original references by the PDBbind team. They all have been double-checked to ensure that they match the complex structures in the Protein Data Bank. Moreover, a "refined set" and a "core set" are compiled as high-quality data sets of protein-ligand complexes for docking/scoring studies.

References

External links http://www.pdbbind.org.cn/

Worked examples

Example 1 — a first encounter with PDBbind database

Start with the simplest possible case. Write down what PDBbind database 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 PDBbind database 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 PDBbind database 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 PDBbind database

In research: PDBbind database 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 PDBbind database 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: PDBbind database 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 PDBbind database 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 PDBbind database in 20 minutes

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

Frequently asked questions

What is PDBbind database in simple terms?

Why does PDBbind database 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 PDBbind database?

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 PDBbind database.