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Biomolecular structure

Index 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. [1]

90 relations: Alpha helix, Amino acid, Atom, Base pair, Bessel function, Beta sheet, Bioinformatics, Biomolecular engineering, Biomolecular structure, Biopolymer, Biotechnology, CASP, Chromatin, Comparison of nucleic acid simulation software, Cryogenic electron microscopy, Curvature, Differential geometry, Dihedral angle, DNA, Drug design, DSSP (hydrogen bond estimation algorithm), Enzyme, Evolution, Fourier transform, Gene structure, Histone, Homology (biology), Hydrogen bond, Intrinsic termination, Kaj Ulrik Linderstrøm-Lang, Kozak consensus sequence, Lipid, List of RNA structure prediction software, LSm, Macromolecule, Medicine, Molecular model, Molecule, Monomer, Non-coding RNA, NP-completeness, Nuclear magnetic resonance spectroscopy, Nucleic acid, Nucleic acid design, Nucleic acid sequence, Nucleic acid structure, Nucleic acid structure determination, Nucleic acid structure prediction, Nucleic acid tertiary structure, Nucleobase, ..., Nucleotide, Paracrystalline, Patterson function, Polyphenol, Polysaccharide, Protein, Protein Data Bank (file format), Protein design, Protein primary structure, Protein structure, Protein subunit, Pseudoknot, Ramachandran plot, Rational design, Raymond Gosling, Ribosome, RNA, RNA polymerase III, Rosalind Franklin, Sequence motif, Shine-Dalgarno sequence, Small nucleolar RNA, Small nucleolar RNA U3, Spliceosome, Stanford University, Stem-loop, Stereochemistry, Tetraloop, Theoretical chemistry, Thymus, Torsion of a curve, Transfer RNA, U1 spliceosomal RNA, U12 minor spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, U6 spliceosomal RNA, X-ray crystallography, X-ray scattering techniques. Expand index (40 more) »

Alpha helix

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a righthand-spiral conformation (i.e. helix) in which every backbone N−H group donates a hydrogen bond to the backbone C.

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Amino acid

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid.

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An atom is the smallest constituent unit of ordinary matter that has the properties of a chemical element.

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Base pair

A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds.

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Bessel function

Bessel functions, first defined by the mathematician Daniel Bernoulli and then generalized by Friedrich Bessel, are the canonical solutions of Bessel's differential equation for an arbitrary complex number, the order of the Bessel function.

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Beta sheet

The β-sheet (also β-pleated sheet) is a common motif of regular secondary structure in proteins.

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Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data.

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Biomolecular engineering

Biomolecular engineering is the application of engineering principles and practices to the purposeful manipulation of molecules of biological origin.

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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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Biopolymers are polymers produced by living organisms; in other words, they are polymeric biomolecules.

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Biotechnology is the broad area of science involving living systems and organisms to develop or make products, or "any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use" (UN Convention on Biological Diversity, Art. 2).

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Critical Assessment of protein Structure Prediction, or CASP, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994.

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Chromatin is a complex of macromolecules found in cells, consisting of DNA, protein, and RNA.

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Comparison of nucleic acid simulation software

This is a list of computer programs that are used for nucleic acids simulations.

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Cryogenic electron microscopy

Electron cryomicroscopy (CryoEM) is an electron microscopy (EM) technique where the sample is cooled to cryogenic temperatures.

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In mathematics, curvature is any of a number of loosely related concepts in different areas of geometry.

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Differential geometry

Differential geometry is a mathematical discipline that uses the techniques of differential calculus, integral calculus, linear algebra and multilinear algebra to study problems in geometry.

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Dihedral angle

A dihedral angle is the angle between two intersecting planes.

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Deoxyribonucleic acid (DNA) is a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses.

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Drug design

Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target.

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DSSP (hydrogen bond estimation algorithm)

The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein.

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Enzymes are macromolecular biological catalysts.

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Evolution is change in the heritable characteristics of biological populations over successive generations.

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Fourier transform

The Fourier transform (FT) decomposes a function of time (a signal) into the frequencies that make it up, in a way similar to how a musical chord can be expressed as the frequencies (or pitches) of its constituent notes.

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Gene structure

Gene structure is the organisation of specialised sequence elements within a gene.

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In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes.

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Homology (biology)

In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa.

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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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Intrinsic termination

Intrinsic termination (also called Rho-independent termination) is a mechanism in prokaryotes that causes RNA transcription to stop and release the newly made RNA.

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Kaj Ulrik Linderstrøm-Lang

Kaj Ulrik Linderstrøm-Lang (29 November 1896 – 25 May 1959) was a Danish protein scientist, who was the director of the Carlsberg Laboratory from 1939 until his death.

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Kozak consensus sequence

The Kozak consensus sequence, Kozak consensus or Kozak sequence is a sequence which occurs on eukaryotic mRNA and has the consensus (gcc)gccRccAUGG.

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In biology and biochemistry, a lipid is a biomolecule that is soluble in nonpolar solvents.

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List of RNA structure prediction software

This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction.

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In molecular biology, LSm proteins are a family of RNA-binding proteins found in virtually every cellular organism.

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A macromolecule is a very large molecule, such as protein, commonly created by the polymerization of smaller subunits (monomers).

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Medicine is the science and practice of the diagnosis, treatment, and prevention of disease.

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Molecular model

A molecular model, in this article, is a physical model that represents molecules and their processes.

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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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Non-coding RNA

A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein.

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In computational complexity theory, an NP-complete decision problem is one belonging to both the NP and the NP-hard complexity classes.

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Nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei.

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Nucleic acid

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

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Nucleic acid design

Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation.

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Nucleic acid sequence

A nucleic acid sequence is a succession of letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule.

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Nucleic acid structure

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA.

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Nucleic acid structure determination

Structure probing of nucleic acids is the process by which biochemical techniques are used to determine nucleic acid structure.

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Nucleic acid structure prediction

Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence.

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Nucleic acid tertiary structure

Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer.

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Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids.

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Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth.

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Paracrystalline materials are defined as having short- and medium-range ordering in their lattice (similar to the liquid crystal phases) but lacking crystal-like long-range ordering at least in one direction.

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Patterson function

The Patterson function is used to solve the phase problem in X-ray crystallography.

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Polyphenols (also known as polyhydroxyphenols) are a structural class of mainly natural, but also synthetic or semisynthetic, organic chemicals characterized by the presence of large multiples of phenol structural units.

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Polysaccharides are polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages, and on hydrolysis give the constituent monosaccharides or oligosaccharides.

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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 Data Bank (file format)

The Protein Data Bank (pdb) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank.

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Protein design

Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function.

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Protein primary structure

Protein primary structure is the linear sequence of amino acids in a peptide or protein.

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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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A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem.

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Ramachandran plot

A Ramachandran plot (also known as a Ramachandran diagram or a plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.

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Rational design

In chemical biology and biomolecular engineering, rational design is the strategy of creating new molecules with a certain functionality, based upon the ability to predict how the molecule's structure will affect its behavior through physical models.

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Raymond Gosling

Raymond George Gosling (15 July 1926 – 18 May 2015) was a British scientist.

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The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis (translation).

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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 polymerase III

In eukaryote cells, RNA polymerase III (also called Pol III) transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs.

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Rosalind Franklin

Rosalind Elsie Franklin (25 July 192016 April 1958) was an English chemist and X-ray crystallographer who made contributions to the understanding of the molecular structures of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), viruses, coal, and graphite.

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Sequence motif

In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.

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Shine-Dalgarno sequence

The Shine-Dalgarno (SD) Sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG.

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Small nucleolar RNA

Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs.

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Small nucleolar RNA U3

U3 snoRNA is a non-coding RNA found predominantly in the nucleolus.

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A spliceosome is a large and complex molecular machine found primarily within the splicing speckles of the cell nucleus of eukaryotic cells.

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Stanford University

Stanford University (officially Leland Stanford Junior University, colloquially the Farm) is a private research university in Stanford, California.

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Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA.

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Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms that form the structure of molecules and their manipulation.

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Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices.

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Theoretical chemistry

Theoretical chemistry is a branch of chemistry, which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry, for example, the concept of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, molecule activation etc.

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The thymus is a specialized primary lymphoid organ of the immune system.

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Torsion of a curve

In the elementary differential geometry of curves in three dimensions, the torsion of a curve measures how sharply it is twisting out of the plane of curvature.

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Transfer RNA

A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins.

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U1 spliceosomal RNA

U1 spliceosomal RNA is the small nuclear RNA (snRNA) component of U1 snRNP (small nuclear ribonucleoprotein), an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.

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U12 minor spliceosomal RNA

U12 minor spliceosomal RNA is formed from U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.

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U2 spliceosomal RNA

U2 spliceosomal snRNAs are a species of small nuclear RNA (snRNA) molecules found in the major spliceosomal (Sm) machinery of virtually all-eukaryotic organisms.

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U4 spliceosomal RNA

The U4 small nuclear Ribo-Nucleic Acid (U4 snRNA) is a non-coding RNA component of the major or U2-dependent spliceosome – a eukaryotic molecular machine involved in the splicing of pre-messenger RNA (pre-mRNA).

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U5 spliceosomal RNA

U5 RNA is a non-coding RNA that is a component of both types of known spliceosome.

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U6 spliceosomal RNA

U6 snRNA is the non-coding small nuclear RNA (snRNA) component of U6 snRNP (small nuclear ribonucleoprotein), an RNA-protein complex that combines with other snRNPs, unmodified pre-mRNA, and various other proteins to assemble a spliceosome, a large RNA-protein molecular complex that catalyzes the excision of introns from pre-mRNA.

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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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X-ray scattering techniques

X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystal structure, chemical composition, and physical properties of materials and thin films.

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Biological sequence, Primary sequence, Primary structure, Quaternary structure, Secondary structural, Secondary structure, Tertiary structure, Tertiary structures.


[1] https://en.wikipedia.org/wiki/Biomolecular_structure

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