WHAT IF is a
computer program
A computer program is a sequence or set of instructions in a programming language for a computer to execute. Computer programs are one component of software, which also includes documentation and other intangible components.
A computer progra ...
used in a wide variety of
computation
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm).
Mechanical or electronic devices (or, historically, people) that perform computations are known as '' computers''. An esp ...
al (''
in silico
In biology and other experimental sciences, an ''in silico'' experiment is one performed on computer or via computer simulation. The phrase is pseudo-Latin for 'in silicon' (correct la, in silicio), referring to silicon in computer chips. It ...
'') macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large
molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...
s,
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s,
nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...
s, and their interactions.
History
The first version of the WHAT IF software was developed by Gert Vriend in 1987 at the
University of Groningen
The University of Groningen (abbreviated as UG; nl, Rijksuniversiteit Groningen, abbreviated as RUG) is a public research university of more than 30,000 students in the city of Groningen in the Netherlands. Founded in 1614, the university is the ...
,
Groningen
Groningen (; gos, Grunn or ) is the capital city and main municipality of Groningen province in the Netherlands. The ''capital of the north'', Groningen is the largest place as well as the economic and cultural centre of the northern part of t ...
, Netherlands.
Most of its development occurred during 1989–2000 at the
European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 a ...
(EMBL) in
Heidelberg
Heidelberg (; Palatine German language, Palatine German: ''Heidlberg'') is a city in the States of Germany, German state of Baden-Württemberg, situated on the river Neckar in south-west Germany. As of the 2016 census, its population was 159,914 ...
, 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
Nijmegen (;; Spanish and it, Nimega. Nijmeegs: ''Nimwèège'' ) is the largest city in the Dutch province of Gelderland and tenth largest of the Netherlands as a whole, located on the Waal river close to the German border. It is about 6 ...
, Netherlands.
It is available for in-house use, or as a web-based resource.
, 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
molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bio ...
s, proteins, nucleic acids, and their interactions. One notable use was detecting many millions of errors (often small, but sometimes catastrophic) in
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...
(PDB) files.
WHAT IF also provides an environment for:
homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous p ...
of
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
tertiary structure
Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may int ...
s and
quaternary structure
Protein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also refe ...
s; validating protein structures, notably those deposited in the PDB; correcting
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
structures; visualising
macromolecule
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. ...
s and their interaction partners (for example,
lipid
Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids incl ...
s,
drug
A drug is any chemical substance that causes a change in an organism's physiology or psychology when consumed. Drugs are typically distinguished from food and substances that provide nutritional support. Consumption of drugs can be via inhal ...
s,
ions, and
water
Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as ...
), and manipulating macromolecules interactively.
WHAT IF is compatible with several other
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
software packages, including
YASARA and
Jmol.
See also
*
List of molecular graphics systems
This is a list of notable software systems that are used for visualizing macromolecules.
Key
The tables below indicate which types of data can be visualized in each system:
See also
* Biological data visualization
* Comparison of nucleic ...
*
Molecule editor
A molecule editor is a computer program for creating and modifying representations of chemical structures.
Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ...
External links
*
References
{{Reflist
Molecular modelling software
Bioinformatics software
Protein structure