computer science

WHAT IF software

WHAT IF software 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 WHAT IF software rather than just read about it. In short: WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large molecules, proteins, nucleic acids, and their interactions.

Key takeaways

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

Reference excerpt

WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large molecules, proteins, nucleic acids, and their interactions.

History The first version of the WHAT IF software was developed by Gert Vriend in 1987 at the University of Groningen, Groningen, Netherlands. Most of its development occurred during 1989–2000 at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. Other contributors include Chris Sander, and Wolfgang Kabsch. In 2000, maintenance of the software moved to the Dutch Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, Netherlands. It is available for in-house use, or as a web-based resource. As of February 2022, the original paper describing WHAT IF has been cited more than 4,000 times.

Software WHAT IF provides a flexible environment to display, manipulate, and analyze small molecules, proteins, nucleic acids, and their interactions. One notable use was detecting many millions of errors (often small, but sometimes catastrophic) in Protein Data Bank (PDB) files. WHAT IF also provides an environment for: homology modeling of protein tertiary structures and quaternary structures; validating protein structures, notably those deposited in the PDB; correcting protein structures; visualising macromolecules and their interaction partners (for example, lipids, drugs, ions, and water), and manipulating macromolecules interactively. WHAT IF is compatible with several other bioinformatics software packages, including YASARA and Jmol.

See also List of molecular graphics systems Molecule editor

External links Official website

References

Worked examples

Example 1 — a first encounter with WHAT IF software

Start with the simplest possible case. Write down what WHAT IF software 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 WHAT IF software 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 WHAT IF software 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 WHAT IF software

In research: WHAT IF software 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 WHAT IF software 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: WHAT IF software is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics software, Molecular modelling software, Protein structure, so understanding it makes those chapters shorter.
In everyday life: Look for WHAT IF software 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.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study WHAT IF software in 20 minutes

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

Frequently asked questions

What is WHAT IF software in simple terms?

Why does WHAT IF software 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 WHAT IF software?

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 WHAT IF software.