computer science

ProBiS

ProBiS 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 ProBiS rather than just read about it. In short: ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010 and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin.

Key takeaways

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

Reference excerpt

ProBiS is a computer software which allows prediction of binding sites and their corresponding ligands for a given protein structure. Initially ProBiS was developed as a ProBiS algorithm by Janez Konc and Dušanka Janežič in 2010 and is now available as ProBiS server, ProBiS CHARMMing server, ProBiS algorithm and ProBiS plugin. The name ProBiS originates from the purpose of the software itself, that is to predict for a given Protein structure Binding Sites and their corresponding ligands.

Description ProBiS software started as ProBiS algorithm that detects structurally similar sites on protein surfaces by local surface structure alignment using a fast maximum clique algorithm. The ProBiS algorithm was followed by ProBiS server which provides access to the program ProBiS that detects protein binding sites based on local structural alignments. There are two ProBiS servers available, ProBiS server and ProBiS CHARMMing server. The latter connects ProBiS and CHARMMing servers into one functional unit that enables prediction of protein−ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS CHARMMing server with these additional functions can only be used at National Institutes of Health, USA. Otherwise it acts as a regular ProBiS server. Additionally a ProBiS PyMOL plugin and ProBiS UCSF Chimera plugin have been made. Both plugins are connected via the internet to a newly prepared database of pre-calculated binding site comparisons to allow fast prediction of binding sites in existing proteins from the Protein Data Bank. They enable viewing of predicted binding sites and ligands poses in three-dimensional graphics.

Protein building sites tools

Detect structurally similar binding sites This tool takes as an input a query protein or a binding site. The ProBiS algorithm structurally compares the query independently of sequence or fold with a database of non-redundant protein structures. The output of this tool are a 3D query protein colored by degrees of structural conservation from blue (unconserved) to red (structurally conserved) in Jmol viewer and a table of similar proteins. Pairwise local structural alignment This tool takes as an input two proteins or binding sites. The ProBiS algorithm compares structures based on geometry as well as physicochemical properties and returns their local structural alignment. ProBiS web server RESTful Web Services The ProBiS web server features RESTful (Representational State Transfer) web services to make the binding site similarities and local pairwise alignments for any PDB protein structure easily accessible from any script. ProBiS-Database access ProBiS-Database can be accessed directly from ProBiS (CHARMMing) server, ProBiS-Database widget, which can be included in any web page to provide access to the ProBiS-Database, or RESTful Web Services, which make ProBiS-Database easily accessible from any script.

History ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment (March 2010) ProBiS: A web server for detection of structurally similar protein binding sites (February 2010) ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures (December 2011) ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins (February 2012) Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites (March 2012) ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites (February 2014) ProBiS-Charmming: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites (August 2015)

References

External links ProBiS server

Illustrations

Worked examples

Example 1 — a first encounter with ProBiS

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

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

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

Frequently asked questions

What is ProBiS in simple terms?

Why does ProBiS 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 ProBiS?

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 ProBiS.