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WHAT IF Software
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. , 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 mole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chris Sander (scientist)
Chris Sander is a computational biologist based at the Dana-Farber Cancer Center and Harvard Medical School. Previously he was chair of the Computational Biology Programme at the Memorial Sloan–Kettering Cancer Center in New York City. In 2015, he moved his lab to the Dana–Farber Cancer Institute and the Cell Biology Department at Harvard Medical School. Education Sander originally trained as a physicist receiving his undergraduate degree from the University of Berlin in 1967. After a period studying at the University of California, Berkeley and the Niels Bohr Institute in Copenhagen, he gained his PhD degree in theoretical physics from the State University of New York in 1975. His thesis was titled ''Analytic properties of bound state wave functions''. Research Sander credits his move from theoretical physics to computational biology to Fred Sanger's 1977 landmark paper in ''Nature'', in which the nucleotide sequence of bacteriophage φX174 was published. Sander has made m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not consid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 a solvent). It is vital for all known forms of life, despite not providing food, energy or organic micronutrients. Its chemical formula, H2O, indicates that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. The hydrogen atoms are attached to the oxygen atom at an angle of 104.45°. "Water" is also the name of the liquid state of H2O at standard temperature and pressure. A number of natural states of water exist. It forms precipitation in the form of rain and aerosols in the form of fog. Clouds consist of suspended droplets of water and ice, its solid state. When finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of water is steam or water vapor. Water co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 insufflation (medicine), inhalation, drug injection, injection, smoking, ingestion, absorption (skin), absorption via a dermal patch, patch on the skin, suppository, or sublingual administration, dissolution under the tongue. In pharmacology, a drug is a chemical substance, typically of known structure, which, when administered to a living organism, produces a biological effect. A pharmaceutical drug, also called a medication or medicine, is a chemical substance used to pharmacotherapy, treat, cure, preventive healthcare, prevent, or medical diagnosis, diagnose a disease or to promote well-being. Traditionally drugs were obtained through extraction from medicinal plants, but more recently also by organic synthesis. Pharmaceutical drugs may be used ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 include storing energy, signaling, and acting as structural components of cell membranes. Lipids have applications in the cosmetic and food industries, and in nanotechnology. Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, multilamellar/unilamellar liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or "building-blocks": ketoacyl and isoprene groups. Using this approach, lipids may be divided into eight categories: fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides (derived from condensati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules such as lipids, nanogels and macrocycles. Synthetic fibers and experimental materials such as carbon nanotubes are also examples of macromolecules. Definition The term ''macromolecule'' (''macro-'' + ''molecule'') was coined by Nobel laureate Hermann Staudinger in the 1920s, although his first relevant publication on this field only mentions ''high molecular compounds'' (in excess of 1,000 atoms). At that time the term ''polymer'', as introduced by Berzelius in 1832, had a different meaning from that of today: it simply was another form of isomerism for example with benzene and acetylene and had litt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits. In contrast to the first three levels of protein structure, not all proteins will have a quaternary structure since some proteins function as single units. Protein quaternary structure can also refer to biomolecular complexes of proteins with nucleic acids and other cofactors. Description and examples Many proteins are actually assemblies of multiple polypeptide chains. The quaternary structure refers to the number and arrangement of the protein subunit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.Branden C. and Tooze J. "Introduction to Protein Structure" Garland Publishing, New York. 1990 and 1991. A number of tertiary structures may fold into a quaternary structure.Kyte, J. "Structure in Protein Chemistry." Garland Publishing, New York. 1995. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 60 km south east of Utrecht and 50 km north east of Eindhoven. Nijmegen is the oldest city in the Netherlands, the second to be recognized as such in Roman times, and in 2005 celebrated 2,000 years of existence. Nijmegen became a free imperial city in 1230 and in 1402 a Hanseatic city. Since 1923 it has been a university city with the opening of a Catholic institution now known as the Radboud University Nijmegen. The city is well known for the International Four Days Marches Nijmegen event. Its population in 2022 was 179,000; the municipality is part of the Arnhem–Nijmegen metropolitan area, with 736,107 inhabitants in 2011. Population centres The municipality is formed by the city of Nijmegen, incorporating the former villages of Ha ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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