biology

Human Protein Reference Database

Human Protein Reference 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 Human Protein Reference Database rather than just read about it. In short: The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore, India.

Key takeaways

Human Protein Reference 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 Human Protein Reference Database to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Human Protein Reference Database from memory before moving on to harder problems.

Reference excerpt

The Human Protein Reference Database (HPRD) is a protein database accessible through the Internet. It is closely associated with the premier Indian Non-Profit research organisation Institute of Bioinformatics (IOB), Bangalore, India. This database is a collaborative output of IOB and the Pandey Lab of Johns Hopkins University.

Overview The HPRD is a result of an international collaborative effort between the Institute of Bioinformatics in Bangalore, India and the Pandey lab at Johns Hopkins University in Baltimore, USA. HPRD contains manually curated scientific information pertaining to the biology of most human proteins. Information regarding proteins involved in human diseases is annotated and linked to Online Mendelian Inheritance in Man (OMIM) database. The National Center for Biotechnology Information provides link to HPRD through its human protein databases (e.g. Entrez Gene, RefSeq protein pertaining to genes and proteins. This resource depicts information on human protein functions including protein–protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. Protein annotation information that is catalogued was derived through manual curation using published literature by expert biologists and through bioinformatics analyses of the protein sequence. The protein–protein interaction and subcellular localization data from HPRD have been used to develop a human protein interaction network. Highlights of HPRD as follows:

From 10,000 protein–protein interactions (PPIs) annotated for 3,000 proteins in 2003, HPRD has grown to over 36,500 unique PPIs annotated for 25,000 proteins including 6,360 isoforms by the end of 2007. More than 50% of molecules annotated in HPRD have at least one PPI and 10% have more than 10 PPIs. Experiments for PPIs are broadly grouped into three categories namely in vitro, in vivo and yeast two hybrid (Y2H). Sixty percent of PPIs annotated in HPRD are supported by a single experiment whereas 26% of them are found to have two of the three experimental methods annotated. HPRD contains 18,000 manually curated PTMs data belonging to 26 different types. Phosphorylation is the leading type of modification of protein contributing to 63% of PTM data annotated in HPRD. Glycosylation, proteolytic cleavage and disulfide bridge events are the next leading contributors of PTM data. HPRD data is available for download in tab delimited and XML file formats. HPRD also integrates data from Human Proteinpedia, a community portal for integrating human protein data. The data from HPRD can be freely accessed and used by academic users while commercial entities are required to obtain a license for use. Human Proteinpedia content is freely available for anyone to download and use.

PhosphoMotif Finder PhosphoMotif Finder contains known kinase/phosphatase substrate as well as binding motifs that are curated from the published literature. It reports the PRESENCE of any literature-derived motif in the query sequence. PhosphoMotif Finder does NOT PREDICT any motifs in the query protein sequence using any algorithm or other computational strategies.

Comparison of protein data There are other databases that deal with human proteome (e.g. BioGRID, BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome). Each database has its own style of presenting the data. It is a difficult task for most investigators to compare the voluminous data from these databases in order to conclude strengths and weaknesses of each database. Mathivanan and colleagues tried to address this issue while analyzing protein data by asking various questions. This analysis will help biologists to choose among these databases based on their needs.

References

External links http://www.humanproteinpedia.org Archived 2007-03-14 at the Wayback Machine http://www.hprd.org Archived 2006-04-24 at the Wayback Machine

Worked examples

Example 1 — a first encounter with Human Protein Reference Database

Start with the simplest possible case. Write down what Human Protein Reference 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 Human Protein Reference 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 Human Protein Reference 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 Human Protein Reference Database

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

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

Frequently asked questions

What is Human Protein Reference Database in simple terms?

Why does Human Protein Reference 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 Human Protein Reference 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 Human Protein Reference Database.