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Protein–protein interaction

Index Protein–protein interaction

Protein–protein interactions (PPIs) are the physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by electrostatic forces including the hydrophobic effect. [1]

127 relations: Accessible surface area, Actin, Adipose triglyceride lipase, Adrenal ferredoxin, Affinity chromatography, Allosteric regulation, Alzheimer's disease, Atomic orbital, ATPase, Ångström, Biochemical cascade, Biochemistry, Biological database, Biological network, Biomolecular Object Network Databank, Biomolecular structure, C-terminus, Calmodulin, Calorimetry, Cell cycle, Cell nucleus, Cell type, Cellular differentiation, Coactivator (genetics), Conformational change, Connectivity (graph theory), Consensus sequence, Coulomb's law, Creutzfeldt–Jakob disease, Cyrus Chothia, Cytochrome c, Cytoplasm, Cytoscape, Cytoskeleton, Database of Interacting Proteins, Disulfide, Electric field, Electro-switchable biosurface, Enzyme, Enzyme catalysis, Ephrin receptor, Fluorescence spectroscopy, Gene expression, Gene regulatory network, Genome-wide association study, GRB2, Growth factor, Hemoglobin, Homeobox, Human interactome, ..., Hydrogen bond, Hydrophobic effect, Insulin, Insulin receptor substrate, Interactome, Ion, John Kendrew, LIM domain, Lipolysis, Machine learning, Mass spectrometry, Membrane protein, Membrane transport protein, Metabolic network, Microarray, Molecular dynamics, Molecular machine, Molecular recognition feature, Molecule, Monomer, Muscle contraction, Myoglobin, Myosin, Natural language processing, Non-covalent interactions, Nuclear magnetic resonance, Nuclear pore, Nucleic acid, Oligomer, Parkinson's disease, PARVA, PDZ domain, Perilipin-1, Phosphatidylinositol 4,5-bisphosphate, Phospholipase C, Phosphoserine, Post-translational modification, Proline, Protein, Protein complex, Protein structure, Protein subunit, Protein-fragment complementation assay, Protein–protein interaction prediction, Protein–protein interaction screening, PTK2, Quantum chemistry, Random forest, Reversible process (thermodynamics), RNA, RNA interference, Scattering, Senescence, Sensitivity and specificity, Signal transduction, Skeletal muscle, Social network, Sperm whale, STIM, STRING, Substrate (chemistry), SUMO protein, Surface plasmon resonance, Systems biology, Talin protein, Tandem affinity purification, Threonine, Trypsin, Two-hybrid screening, Tyrosine, Tyrosine kinase, Ubiquitin, Ultracentrifuge, Van der Waals force, X-ray crystallography, Zinc finger, 3did. Expand index (77 more) »

Accessible surface area

The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent.

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Actin is a family of globular multi-functional proteins that form microfilaments.

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Adipose triglyceride lipase

Adipose triglyceride lipase also known as patatin-like phospholipase domain-containing protein 2 is an enzyme that in humans is encoded by the PNPLA2 gene.

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Adrenal ferredoxin

Adrenal ferredoxin (also adrenodoxin (ADX), adrenodoxin, mitochondrial, hepatoredoxin, ferredoxin-1 (FDX1)) is a protein that in humans is encoded by the FDX1 gene.

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Affinity chromatography

Affinity chromatography is a method of separating biochemical mixtures based on a highly specific interaction between antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid.

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Allosteric regulation

In biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site.

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Alzheimer's disease

Alzheimer's disease (AD), also referred to simply as Alzheimer's, is a chronic neurodegenerative disease that usually starts slowly and worsens over time.

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Atomic orbital

In quantum mechanics, an atomic orbital is a mathematical function that describes the wave-like behavior of either one electron or a pair of electrons in an atom.

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ATPases (adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, adenosine 5'-triphosphatase, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3−-ATPase, adenosine triphosphatase) are a class of enzymes that catalyze the decomposition of ATP into ADP and a free phosphate ion.

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The ångström or angstrom is a unit of length equal to (one ten-billionth of a metre) or 0.1 nanometre.

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Biochemical cascade

A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions which are initiated by a stimulus (first messenger) acting on a receptor that is transduced to the cell interior through second messengers (which amplify the initial signal) and ultimately to effector molecules, resulting in a cell response to the initial stimulus.

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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms.

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Biological database

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.

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Biological network

A biological network is any network that applies to biological systems.

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Biomolecular Object Network Databank

The Biomolecular Object Network Databank is a bioinformatics databank containing information on small molecule and, structures and interactions.

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Biomolecular structure

Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.

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The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH).

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Calmodulin (CaM) (an abbreviation for calcium-modulated protein) is a multifunctional intermediate calcium-binding messenger protein expressed in all eukaryotic cells.

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Calorimetry is the science or act of measuring changes in state variables of a body for the purpose of deriving the heat transfer associated with changes of its state due, for example, to chemical reactions, physical changes, or phase transitions under specified constraints.

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Cell cycle

The cell cycle or cell-division cycle is the series of events that take place in a cell leading to its division and duplication of its DNA (DNA replication) to produce two daughter cells.

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Cell nucleus

In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel or seed) is a membrane-enclosed organelle found in eukaryotic cells.

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Cell type

A cell type is a classification used to distinguish between morphologically or phenotypically distinct cell forms within a species.

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Cellular differentiation

In developmental biology, cellular differentiation is the process where a cell changes from one cell type to another.

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Coactivator (genetics)

A coactivator is a type of transcriptional coregulator that binds to an activator (a transcription factor) to increase the rate of transcription of a gene or set of genes.

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Conformational change

In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors.

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Connectivity (graph theory)

In mathematics and computer science, connectivity is one of the basic concepts of graph theory: it asks for the minimum number of elements (nodes or edges) that need to be removed to disconnect the remaining nodes from each other.

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Consensus sequence

In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment.

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Coulomb's law

Coulomb's law, or Coulomb's inverse-square law, is a law of physics for quantifying the amount of force with which stationary electrically charged particles repel or attract each other.

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Creutzfeldt–Jakob disease

Creutzfeldt–Jakob disease (CJD) is a universally fatal brain disorder.

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Cyrus Chothia

Cyrus Homi Chothia (born 19 February 1942) is an emeritus scientist at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) at the University of Cambridge and emeritus fellow of Wolfson College, Cambridge.

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Cytochrome c

The cytochrome complex, or cyt c is a small hemeprotein found loosely associated with the inner membrane of the mitochondrion.

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In cell biology, the cytoplasm is the material within a living cell, excluding the cell nucleus.

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Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data.

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A cytoskeleton is present in all cells of all domains of life (archaea, bacteria, eukaryotes).

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Database of Interacting Proteins

The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins.

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In chemistry, a disulfide refers to a functional group with the structure R−S−S−R′.

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Electric field

An electric field is a vector field surrounding an electric charge that exerts force on other charges, attracting or repelling them.

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Electro-switchable biosurface

An electro-switchable biosurface is a biosensor that can be used in conjunction with alternating or fixed electrical potentials in order to affect change in the structure and position (movement) of charged biomolecules such as DNA, RNA or oligopeptides bound to the biosurface.

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Enzymes are macromolecular biological catalysts.

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Enzyme catalysis

Enzyme catalysis is the increase in the rate of a chemical reaction by the active site of a protein.

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Ephrin receptor

Eph receptors (Ephs, after erythropoietin-producing human hepatocellular receptors) are a group of receptors that are activated in response to binding with Eph receptor-interacting proteins (Ephrins).

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Fluorescence spectroscopy

Fluorescence spectroscopy (also known as fluorometry or spectrofluorometry) is a type of electromagnetic spectroscopy that analyzes fluorescence from a sample.

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Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product.

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Gene regulatory network

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins.

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Genome-wide association study

In genetics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.

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Growth factor receptor-bound protein 2 also known as Grb2 is an adaptor protein involved in signal transduction/cell communication.

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Growth factor

A growth factor is a naturally occurring substance capable of stimulating cellular growth, proliferation, healing, and cellular differentiation.

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Hemoglobin (American) or haemoglobin (British); abbreviated Hb or Hgb, is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates (with the exception of the fish family Channichthyidae) as well as the tissues of some invertebrates.

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A homeobox is a DNA sequence, around 180 base pairs long, found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis) in animals, fungi and plants.

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Human interactome

The human interactome is the set of protein–protein interactions (the interactome) that occur in human cells.

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Hydrogen bond

A hydrogen bond is a partially electrostatic attraction between a hydrogen (H) which is bound to a more electronegative atom such as nitrogen (N), oxygen (O), or fluorine (F), and another adjacent atom bearing a lone pair of electrons.

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Hydrophobic effect

The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules.

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Insulin (from Latin insula, island) is a peptide hormone produced by beta cells of the pancreatic islets; it is considered to be the main anabolic hormone of the body.

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Insulin receptor substrate

Insulin receptor substrate (IRS) is an important ligand in the insulin response of human cells.

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In molecular biology, an interactome is the whole set of molecular interactions in a particular cell.

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An ion is an atom or molecule that has a non-zero net electrical charge (its total number of electrons is not equal to its total number of protons).

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John Kendrew

Sir John Cowdery Kendrew, (24 March 1917 – 23 August 1997) was an English biochemist and crystallographer who shared the 1962 Nobel Prize in Chemistry with Max Perutz; their group in the Cavendish Laboratory investigated the structure of heme-containing proteins.

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LIM domain

LIM domains are protein structural domains, composed of two contiguous zinc finger domains, separated by a two-amino acid residue hydrophobic linker.

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Lipolysis is the breakdown of lipids and involves hydrolysis of triglycerides into glycerol and free fatty acids.

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Machine learning

Machine learning is a subset of artificial intelligence in the field of computer science that often uses statistical techniques to give computers the ability to "learn" (i.e., progressively improve performance on a specific task) with data, without being explicitly programmed.

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Mass spectrometry

Mass spectrometry (MS) is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio.

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Membrane protein

Membrane proteins are proteins that interact with, or are part of, biological membranes.

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Membrane transport protein

A membrane transport protein (or simply transporter) is a membrane protein involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane.

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Metabolic network

A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell.

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A microarray is a multiplex lab-on-a-chip.

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Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules.

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Molecular machine

A molecular machine, nanite, or nanomachine, refers to any discrete number of molecular components that produce quasi-mechanical movements (output) in response to specific stimuli (input).

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Molecular recognition feature

Molecular recognition features (MoRFs) are small (10-70 residues) intrinsically disordered regions in proteins that undergo a disorder-to-order transition upon binding to their partners.

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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds.

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A monomer (mono-, "one" + -mer, "part") is a molecule that "can undergo polymerization thereby contributing constitutional units to the essential structure of a macromolecule".

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Muscle contraction

Muscle contraction is the activation of tension-generating sites within muscle fibers.

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Myoglobin (symbol Mb or MB) is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals.

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Myosins are a superfamily of motor proteins best known for their roles in muscle contraction and in a wide range of other motility processes in eukaryotes.

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Natural language processing

Natural language processing (NLP) is an area of computer science and artificial intelligence concerned with the interactions between computers and human (natural) languages, in particular how to program computers to process and analyze large amounts of natural language data.

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Non-covalent interactions

A non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule.

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Nuclear magnetic resonance

Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a magnetic field absorb and re-emit electromagnetic radiation.

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Nuclear pore

Nuclear pore complexes are large protein complexes that span the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus.

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Nucleic acid

Nucleic acids are biopolymers, or small biomolecules, essential to all known forms of life.

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An oligomer (oligo-, "a few" + -mer, "parts") is a molecular complex of chemicals that consists of a few monomer units, in contrast to a polymer, where the number of monomers is, in principle, infinite.

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Parkinson's disease

Parkinson's disease (PD) is a long-term degenerative disorder of the central nervous system that mainly affects the motor system.

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Alpha-parvin is a protein that in humans is encoded by the PARVA gene.

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PDZ domain

The PDZ domain is a common structural domain of 80-90 amino-acids found in the signaling proteins of bacteria, yeast, plants, viruses and animals.

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Perilipin, also known as lipid droplet-associated protein, Perilipin 1, or PLIN, is a protein that, in humans, is encoded by the PLIN gene.

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Phosphatidylinositol 4,5-bisphosphate

Phosphatidylinositol 4,5-bisphosphate or PtdIns(4,5)P2, also known simply as PIP2 or PI(4,5)P2, is a minor phospholipid component of cell membranes.

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Phospholipase C

Phospholipase C (PLC) is a class of membrane-associated enzymes that cleave phospholipids just before the phosphate group (see figure).

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Phosphoserine (abbreviated as SEP or J) is an ester of serine and phosphoric acid.

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Post-translational modification

Post-translational modification (PTM) refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis.

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Proline (symbol Pro or P) is a proteinogenic amino acid that is used in the biosynthesis of proteins.

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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.

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Protein complex

A protein complex or multiprotein complex is a group of two or more associated polypeptide chains.

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Protein structure

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule.

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Protein subunit

In structural biology, a protein subunit is a single protein molecule that assembles (or "coassembles") with other protein molecules to form a protein complex.

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Protein-fragment complementation assay

Within the field of molecular biology, a protein-fragment complementation assay, or PCA, is a method for the identification and quantification of protein–protein interactions.

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Protein–protein interaction prediction

Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins.

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Protein–protein interaction screening

The screening of protein–protein interactions refers to the identification of protein interactions with high-throughput screening methods such as computer- and/or robot-assisted plate reading, flow cytometry analyzing.

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PTK2 protein tyrosine kinase 2 (PTK2), also known as focal adhesion kinase (FAK), is a protein that, in humans, is encoded by the PTK2 gene.

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Quantum chemistry

Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems.

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Random forest

Random forests or random decision forests are an ensemble learning method for classification, regression and other tasks, that operate by constructing a multitude of decision trees at training time and outputting the class that is the mode of the classes (classification) or mean prediction (regression) of the individual trees.

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Reversible process (thermodynamics)

In thermodynamics, a reversible process is a process whose direction can be "reversed" by inducing infinitesimal changes to some property of the system via its surroundings, with no increase in entropy.

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Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes.

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RNA interference

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules.

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Scattering is a general physical process where some forms of radiation, such as light, sound, or moving particles, are forced to deviate from a straight trajectory by one or more paths due to localized non-uniformities in the medium through which they pass.

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Senescence or biological ageing is the gradual deterioration of function characteristic of most complex lifeforms, arguably found in all biological kingdoms, that on the level of the organism increases mortality after maturation.

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Sensitivity and specificity

Sensitivity and specificity are statistical measures of the performance of a binary classification test, also known in statistics as a classification function.

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Signal transduction

Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular response.

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Skeletal muscle

Skeletal muscle is one of three major muscle types, the others being cardiac muscle and smooth muscle.

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Social network

A social network is a social structure made up of a set of social actors (such as individuals or organizations), sets of dyadic ties, and other social interactions between actors.

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Sperm whale

The sperm whale (Physeter macrocephalus) or cachalot is the largest of the toothed whales and the largest toothed predator.

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STIM, Svenska Tonsättares Internationella Musikbyrå, is a Swedish collecting society for songwriters, composers and music publisher.

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In molecular biology, STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a biological database and web resource of known and predicted protein–protein interactions.

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Substrate (chemistry)

In chemistry, a substrate is typically the chemical species being observed in a chemical reaction, which reacts with a reagent to generate a product.

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SUMO protein

Small Ubiquitin-like Modifier (or SUMO) proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function.

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Surface plasmon resonance

Surface plasmon resonance (SPR) is the resonant oscillation of conduction electrons at the interface between negative and positive permittivity material stimulated by incident light.

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Systems biology

Systems biology is the computational and mathematical modeling of complex biological systems.

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Talin protein

Talin is a high-molecular-weight cytoskeletal protein concentrated at regions of cell–substratum contact and, in lymphocytes, at cell–cell contacts.

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Tandem affinity purification

Tandem affinity purification (TAP) is a purification technique for studying protein–protein interactions.

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Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins.

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Trypsin is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins.

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Two-hybrid screening

Two-hybrid screening (originally known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions (PPIs) and protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively.

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Tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins.

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Tyrosine kinase

A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell.

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Ubiquitin is a small (8.5 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e. it occurs ''ubiquitously''.

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The ultracentrifuge is a centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as (approx.). There are two kinds of ultracentrifuges, the preparative and the analytical ultracentrifuge.

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Van der Waals force

In molecular physics, the van der Waals forces, named after Dutch scientist Johannes Diderik van der Waals, are distance-dependent interactions between atoms or molecules.

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X-ray crystallography

X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.

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Zinc finger

A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold.

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The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein interactions for which a high-resolution 3D structure is known.

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[1] https://en.wikipedia.org/wiki/Protein–protein_interaction

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