computer science

RaptorX

RaptorX is a computer science 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 RaptorX rather than just read about it. In short: RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction.

Key takeaways

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

Reference excerpt

RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Like other remote homology recognition and protein threading techniques, RaptorX is able to regularly generate reliable protein models when the widely used PSI-BLAST cannot. However, RaptorX is also significantly different from profile-based methods (e.g., HHPred and Phyre2) in that RaptorX excels at modeling of protein sequences without a large number of sequence homologs by exploiting structure information. RaptorX Server has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods.

Description The RaptorX project was started in 2008 and RaptorX Server was released to the public in 2011.

Standard usage After pasting a protein sequence into the RaptorX submission form, a user will typically wait a couple of hours (depending on sequence length) for a prediction to complete. An email is sent to the user together with a link to a web page of results. RaptorX Server currently generates the following results: 3-state and 8-state secondary structure prediction, sequence-template alignment, 3D structure prediction, solvent accessibility prediction, disorder prediction and binding site prediction. The predicted results are displayed to support visual examination. The result files are also available for download. RaptorX Server also produces some confidence scores indicating the quality of the predicted 3D models (in the absence of their corresponding native structures). For example, it produces P-value for relative global quality of a 3D model, global distance test (GDT) and uGDT (unnormalized-GDT) for absolute global quality of a 3D model and per-position root mean square deviation (RMSD) for absolute local quality at each residue of a 3D model.

Applications and performance Applications of RaptorX include protein structure prediction, function prediction, protein sequence-structure alignment, evolutionary classification of proteins, guiding site-directed mutagenesis and solving protein crystal structures by molecular replacement. In the Critical Assessment of Structure Prediction (CASP) CASP9 blind protein structure prediction experiment, RaptorX was ranked 2nd out of about 80 automatic structure prediction servers. RaptorX also generated the best alignments for the 50 hardest CASP9 template-based modeling (TBM) targets. In CASP10, RaptorX is the only server group among the top 10 human/server groups for the 15 most difficult CASP10 TBM targets.

History RaptorX is the successor to the RAPTOR protein structure prediction system. RAPTOR was designed and developed by Dr. Jinbo Xu and Dr. Ming Li at the University of Waterloo. RaptorX was designed and developed by a research group led by Prof. Jinbo Xu at the Toyota Technological Institute branch at Chicago.

See also Protein structure prediction CASP List of protein structure prediction software

References

External links Official website CASP website other structural bioinformatics software

Worked examples

Example 1 — a first encounter with RaptorX

Start with the simplest possible case. Write down what RaptorX claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, 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 RaptorX 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 RaptorX 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 RaptorX

In research: RaptorX appears in computer science 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 RaptorX 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: RaptorX is common in secondary-school and first-year university syllabi. It links to neighbouring topics Computational science, Structural bioinformatics software, so understanding it makes those chapters shorter.
In everyday life: Look for RaptorX 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 RaptorX in 20 minutes

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

Frequently asked questions

What is RaptorX in simple terms?

RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction.

Why does RaptorX matter?

Because it connects several computer science 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 RaptorX?

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 RaptorX.