Simplified molecular-input line-entry system
The simplified molecular-input line-entry system is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules; the original SMILES specification was initiated in the 1980s. It has since been extended. In 2007, an open standard called. Other linear notations include the Wiswesser line notation, ROSDAL, SYBYL Line Notation; the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo and Albert Leo and Corwin Hansch for supporting the work, Arthur Weininger and Jeremy Scofield for assistance in programming the system." The Environmental Protection Agency funded the initial project to develop SMILES. It has since been modified and extended by others, most notably by Daylight Chemical Information Systems.
In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other'linear' notations include the Wiswesser Line Notation, ROSDAL and SLN. In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is considered to have the advantage of being more human-readable than InChI; the term SMILES refers to a line notation for encoding molecular structures and specific instances should be called SMILES strings. However, the term SMILES is commonly used to refer to both a single SMILES string and a number of SMILES strings; the terms "canonical" and "isomeric" can lead to some confusion when applied to SMILES. The terms are not mutually exclusive. A number of valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol. Algorithms have been developed to generate the same SMILES string for a given molecule; this SMILES is unique for each structure, although dependent on the canonicalization algorithm used to generate it, is termed the canonical SMILES.
These algorithms first convert the SMILES to an internal representation of the molecular structure. Various algorithms for generating canonical SMILES have been developed and include those by Daylight Chemical Information Systems, OpenEye Scientific Software, MEDIT, Chemical Computing Group, MolSoft LLC, the Chemistry Development Kit. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database; the original paper that described the CANGEN algorithm claimed to generate unique SMILES strings for graphs representing molecules, but the algorithm fails for a number of simple cases and cannot be considered a correct method for representing a graph canonically. There is no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, double bond geometry; these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES.
A notable feature of these rules is. The term isomeric SMILES is applied to SMILES in which isotopes are specified. In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph; the chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree; the resultant SMILES form depends on the choices: of the bonds chosen to break cycles, of the starting atom used for the depth-first traversal, of the order in which branches are listed when encountered. Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as for gold. Brackets may be omitted in the common case of atoms which: are in the "organic subset" of B, C, N, O, P, S, F, Cl, Br, or I, have no formal charge, have the number of hydrogens attached implied by the SMILES valence model, are the normal isotopes, are not chiral centers.
All other elements must be enclosed in brackets, have charges and hydrogens shown explicitly. For instance, the SMILES for water may be written as either O or. Hydrogen may be written as a separate atom; when brackets are used, the symbol H is added if the atom in brackets is bonded to one or more hydrogen, followed by the number of hydrogen atoms if greater than 1 by the sign + for a positive charge or by - for a negative charge. For example, for ammonium. If there is more than one charge, it is written as digit.
Glycosidic bond
In chemistry, a glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be another carbohydrate. A glycosidic bond is formed between the hemiacetal or hemiketal group of a saccharide and the hydroxyl group of some compound such as an alcohol. A substance containing a glycosidic bond is a glycoside; the term'glycoside' is now extended to cover compounds with bonds formed between hemiacetal groups of sugars and several chemical groups other than hydroxyls, such as -SR, -SeR, -NR1R2, or -CR1R2R3. In occurring glycosides, the compound ROH from which the carbohydrate residue has been removed is termed the aglycone, the carbohydrate residue itself is sometimes referred to as the'glycone'. Glycosidic bonds of the form discussed above are known as O-glycosidic bonds, in reference to the glycosidic oxygen that links the glycoside to the aglycone or reducing end sugar. In analogy, one considers S-glycosidic bonds, where the oxygen of the glycosidic bond is replaced with a sulfur atom.
In the same way, N-glycosidic bonds, have the glycosidic bond oxygen replaced with nitrogen. Substances containing N-glycosidic bonds are known as glycosylamines. C-glycosyl bonds have the glycosidic oxygen replaced by a carbon. All of these modified glycosidic bonds have different susceptibility to hydrolysis, in the case of C-glycosyl structures, they are more resistant to hydrolysis. One distinguishes between α- and β-glycosidic bonds based on the relative stereochemistry of the anomeric position and the stereocenter furthest from C1 in the saccharide. An α-glycosidic bond is formed when both carbons have the same stereochemistry, whereas a β-glycosidic bond occurs when the two carbons have different stereochemistry. One complicating issue is that the alpha and beta conformations were defined based on the relative orientation of the major constituents in a Haworth projection. In this case, for D-sugars, a beta conformation would see the major constituent at each carbon drawn above the plane of the ring, while alpha would see the anomeric constituent below the ring.
For L-sugars, the definitions would necessarily, reverse. This is worth noting as these older definitions still permeate the literature and can lead to confusion. Pharmacologists join substances to glucuronic acid via glycosidic bonds in order to increase their water solubility. Many other glycosides have important physiological functions. Nüchter et al. have shown a new approach to Fischer Glycosylation. Employing a microwave oven equipped with refluxing apparatus in a rotor reactor with pressure bombs, Nüchter et al. were able to achieve 100% yield of α- and β-D-glucosides. This method can be performed on a multi-kilogram scale. Vishal Y Joshi's method Joshi et al. propose the Koenigs-Knorr method in the stereoselective synthesis of alkyl D-glucopyranosides via glycosylation, with the exception of using lithium carbonate, less expensive and toxic than the conventional method of using silver or mercury salts. D-glucose is first protected by forming the peracetate by addition of acetic anhydride in acetic acid, addition of hydrogen bromide which brominates at the 5-position.
On addition of the alcohol ROH and lithium carbonate, the OR replaces the bromine and on deprotecting the acetylated hydroxyls the product is produced in high purity. It was suggested by Joshi et al. that lithium acts as the nucleophile that attacks the carbon at the 5-position and through a transition state the alcohol is substituted for the bromine group. Advantages of this method as well as its stereoselectivity and low cost of the lithium salt include that it can be done at room temperature and its yield compares well with the conventional Koenigs-Knorr method. Glycoside hydrolases, are enzymes. Glycoside hydrolases can act either on α- or on β-glycosidic bonds, but not on both; this specificity allows researchers to obtain glycosides in high epimeric excess, one example being Wen-Ya Lu's conversion of D-Glucose to Ethyl β-D-glucopyranoside using naturally-derived glucosidase. It is worth noting that Wen-Ya Lu utilized glucosidase in a reverse manner opposite to the enzyme's biological functionality: Before monosaccharide units are incorporated into glycoproteins, polysaccharides, or lipids in living organisms, they are first "activated" by being joined via a glycosidic bond to the phosphate group of a nucleotide such as uridine diphosphate, guanosine diphosphate, thymidine diphosphate, or cytidine monophosphate.
These activated biochemical intermediates are known as sugar nucleotides or sugar donors. Many biosynthetic pathways use mono- or oligosaccharides activated by a diphosphate linkage to lipids, such as dolichol; these activated donors are substrates for enzymes known as glycosyltransferases, which transfer the sugar unit from the activated donor to an accepting nucleophile. Different biocatalytic approaches has been developed toward the synthesis of glycosides in the past decades, which using “glycosyltransferases” and “glycoside hydrolases” are among the most common catalysis; the former needs expensive materials and the often shows low yields, De Winter et al. investigated use of cellobiose phosphorylase toward synthesis of alpha-glycosides in ionic liquids. The best condition f
Transfer RNA
A transfer RNA is an adaptor molecule composed of RNA 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. TRNA does this by carrying an amino acid to the protein synthetic machinery of a cell as directed by a 3-nucleotide sequence in a messenger RNA; as such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code. While the specific nucleotide sequence of an mRNA specifies which amino acids are incorporated into the protein product of the gene from which the mRNA is transcribed, the role of tRNA is to specify which sequence from the genetic code corresponds to which amino acid; the mRNA encodes a protein as a series of contiguous codons, each of, recognized by a particular tRNA. One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon; the anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis.
On the other end of the tRNA is a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA; because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors, which aid in association of the tRNA with the ribosome, synthesis of the new polypeptide, translocation of the ribosome along the mRNA. If the tRNA's anticodon matches the mRNA, another tRNA bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly delivered tRNA, a reaction catalyzed by the ribosome.
A large number of the individual nucleotides in a tRNA molecule may be chemically modified by methylation or deamidation. These unusual bases sometimes affect the tRNA's interaction with ribosomes and sometimes occur in the anticodon to alter base-pairing properties; the structure of tRNA can be decomposed into its primary structure, its secondary structure, its tertiary structure. The cloverleaf structure becomes the 3D L-shaped structure through coaxial stacking of the helices, a common RNA tertiary structure motif; the lengths of each arm, as well as the loop'diameter', in a tRNA molecule vary from species to species. The tRNA structure consists of the following: A 5'-terminal phosphate group; the acceptor stem is a 7- to 9-base pair stem made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal nucleotide. In general, such 3'-terminal tRNA-like structures are referred to as'genomic tags'; the acceptor stem may contain non-Watson-Crick base pairs. The CCA tail is a cytosine-cytosine-adenine sequence at the 3' end of the tRNA molecule.
The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases, to form aminoacyl-tRNA, is covalently bonded to the 3'-hydroxyl group on the CCA tail. This sequence critical in translation. In prokaryotes, the CCA sequence is transcribed in some tRNA sequences. In most prokaryotic tRNAs and eukaryotic tRNAs, the CCA sequence is added during processing and therefore does not appear in the tRNA gene; the D arm is a 4- to 6-bp stem ending in a loop that contains dihydrouridine. The anticodon arm is a 5-bp stem; the tRNA 5'-to-3' primary structure contains the anticodon but in reverse order, since 3'-to-5' directionality is required to read the mRNA from 5'-to-3'. The T arm is a 4- to 5- bp stem containing the sequence TΨC where Ψ is pseudouridine, a modified uridine. Bases that have been modified by methylation, occur in several positions throughout the tRNA; the first anticodon base, or wobble-position, is sometimes modified to inosine, uridine-5-oxyacetic acid, 5-methylaminomethyl-2-thiouridine, or lysidine.
An anticodon is a unit made up of three nucleotides that correspond to the three bases of the codon on the mRNA. Each tRNA contains a distinct anticodon triplet sequence that can form 3 complementary base pairs to one or more codons for an amino acid; some anticodons can pair with more than one codon due to a phenomenon known as wobble base pairing. The first nucleotide of the anticodon is one not found on mRNA: inosine, which can hydrogen bond to more than one base in the corresponding codon position. In the genetic code, it is common for a single amino acid to be specified by all four third-position possibilities, or at least by both pyrimidines and purines. Other modified nucleotides may appear at the first anticodon position—sometimes known as the "wobble position"—resulting in subtle changes to the genetic code, as for example in mitochondria. Per cell, 61 types of tRNA would be required to provide a one-to-one correspondence between tRNA molecules and codons that specify amino acids, as there are 61 sense codons of the standard genetic c
Enzyme
Enzymes are macromolecular biological catalysts. Enzymes accelerate chemical reactions; the molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. All metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps; the study of enzymes is called enzymology and a new field of pseudoenzyme analysis has grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, reflected in their amino acid sequences and unusual'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins; the latter are called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction rate by lowering its activation energy; some enzymes can make their conversion of substrate to product occur many millions of times faster.
An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, many enzymes are denatured when exposed to excessive heat, losing their structure and catalytic properties; some enzymes are used commercially, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.
By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. A few decades when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms, he wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."In 1877, German physiologist Wilhelm Kühne first used the term enzyme, which comes from Greek ἔνζυμον, "leavened" or "in yeast", to describe this process. The word enzyme was used to refer to nonliving substances such as pepsin, the word ferment was used to refer to chemical activity produced by living organisms.
Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts when there were no living yeast cells in the mixture, he named the enzyme that brought about the fermentation of sucrose "zymase". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate or to the type of reaction; the biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others argued that proteins were carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner crystallized it; the conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin and chymotrypsin.
These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized allowed their structures to be solved by x-ray crystallography; this was first done for lysozyme, an enzyme found in tears and egg whites that digests the coating of some bacteria. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. An enzyme's name is derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes; the International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. The first number broadly classifies the enzyme based on its mechanism; the top-level classification is: EC 1, Oxidoreductases: catalyze oxidation/reducti
Nature (journal)
Nature is a British multidisciplinary scientific journal, first published on 4 November 1869. It is one of the most recognizable scientific journals in the world, was ranked the world's most cited scientific journal by the Science Edition of the 2010 Journal Citation Reports and is ascribed an impact factor of 40.137, making it one of the world's top academic journals. It is one of the few remaining academic journals that publishes original research across a wide range of scientific fields. Research scientists are the primary audience for the journal, but summaries and accompanying articles are intended to make many of the most important papers understandable to scientists in other fields and the educated public. Towards the front of each issue are editorials and feature articles on issues of general interest to scientists, including current affairs, science funding, scientific ethics and research breakthroughs. There are sections on books and short science fiction stories; the remainder of the journal consists of research papers, which are dense and technical.
Because of strict limits on the length of papers the printed text is a summary of the work in question with many details relegated to accompanying supplementary material on the journal's website. There are many fields of research in which important new advances and original research are published as either articles or letters in Nature; the papers that have been published in this journal are internationally acclaimed for maintaining high research standards. Fewer than 8% of submitted papers are accepted for publication. In 2007 Nature received the Prince of Asturias Award for Humanity; the enormous progress in science and mathematics during the 19th century was recorded in journals written in German or French, as well as in English. Britain underwent enormous technological and industrial changes and advances in the latter half of the 19th century. In English the most respected scientific journals of this time were the refereed journals of the Royal Society, which had published many of the great works from Isaac Newton, Michael Faraday through to early works from Charles Darwin.
In addition, during this period, the number of popular science periodicals doubled from the 1850s to the 1860s. According to the editors of these popular science magazines, the publications were designed to serve as "organs of science", in essence, a means of connecting the public to the scientific world. Nature, first created in 1869, was not the first magazine of its kind in Britain. One journal to precede Nature was Recreative Science: A Record and Remembrancer of Intellectual Observation, created in 1859, began as a natural history magazine and progressed to include more physical observational science and technical subjects and less natural history; the journal's name changed from its original title to Intellectual Observer: A Review of Natural History, Microscopic Research, Recreative Science and later to the Student and Intellectual Observer of Science and Art. While Recreative Science had attempted to include more physical sciences such as astronomy and archaeology, the Intellectual Observer broadened itself further to include literature and art as well.
Similar to Recreative Science was the scientific journal Popular Science Review, created in 1862, which covered different fields of science by creating subsections titled "Scientific Summary" or "Quarterly Retrospect", with book reviews and commentary on the latest scientific works and publications. Two other journals produced in England prior to the development of Nature were the Quarterly Journal of Science and Scientific Opinion, established in 1864 and 1868, respectively; the journal most related to Nature in its editorship and format was The Reader, created in 1864. These similar journals all failed; the Popular Science Review survived longest, lasting 20 years and ending its publication in 1881. The Quarterly Journal, after undergoing a number of editorial changes, ceased publication in 1885; the Reader terminated in 1867, Scientific Opinion lasted a mere 2 years, until June 1870. Not long after the conclusion of The Reader, a former editor, Norman Lockyer, decided to create a new scientific journal titled Nature, taking its name from a line by William Wordsworth: "To the solid ground of nature trusts the Mind that builds for aye".
First owned and published by Alexander Macmillan, Nature was similar to its predecessors in its attempt to "provide cultivated readers with an accessible forum for reading about advances in scientific knowledge." Janet Browne has proposed that "far more than any other science journal of the period, Nature was conceived and raised to serve polemic purpose." Many of the early editions of Nature consisted of articles written by members of a group that called itself the X Club, a group of scientists known for having liberal and somewhat controversial scientific beliefs relative to the time period. Initiated by Thomas Henry Huxley, the group consisted of such important scientists as Joseph Dalton Hooker, Herbert Spencer, John Tyndall, along with another five scientists and mathematicians, it was in part its scientific liberality that made Nature a longer-lasti
RNA
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding and expression of genes. RNA and DNA are nucleic acids, along with lipids and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome; some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function in which RNA molecules direct the assembly of proteins on ribosomes; this process uses transfer RNA molecules to deliver amino acids to the ribosome, where ribosomal RNA links amino acids together to form proteins.
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed of RNA; each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, cytosine, guanine, or uracil. Adenine and guanine are purines and uracil are pyrimidines. A phosphate group is attached to the 5' position of the next; the phosphate groups have a negative charge each. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar; the presence of this functional group causes the helix to take the A-form geometry, although in single strand dinucleotide contexts, RNA can also adopt the B-form most observed in DNA. The A-form geometry results in a deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases, but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, ribothymidine are found in various places.
Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code. There are more than 100 other occurring modified nucleosides; the greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose present in rRNA are the most common. The specific roles of many of these modifications in RNA are not understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function; the functional form of single-stranded RNA molecules, just like proteins requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule; this leads to several recognizable "domains" of secondary structure like hairpin loops and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. The occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by RNase. Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule; this is done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology. Synthesis of RNA is catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA; the DNA double helix is unwound by the helicase activity of the enzyme. The enzyme progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occ
Jmol
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g. in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Unix, if Java is installed, it is free and open-source software released under a GNU Lesser General Public License version 2.0. A standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways. For example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a wide range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile, Chemical Markup Language. There is a JavaScript-only version, JSmol, that can be used on computers with no Java.
The Jmol applet, among other abilities, offers an alternative to the Chime plug-in, no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol operates on a wide variety of platforms. For example, Jmol is functional in Mozilla Firefox, Internet Explorer, Google Chrome, Safari. Chemistry Development Kit Comparison of software for molecular mechanics modeling Jmol extension for MediaWiki List of molecular graphics systems Molecular graphics Molecule editor Proteopedia PyMOL SAMSON Official website Wiki with listings of websites and moodles Willighagen, Egon. "Fast and Scriptable Molecular Graphics in Web Browsers without Java3D". Doi:10.1038/npre.2007.50.1
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