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Jmol is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: urease) and MolMol (example: SH2 domain) also produce ribbon images. KiNG [11] is the Java-based successor to Mage (examples: α-hemolysin top view and ...
When Pauling and Corey first proposed the alpha sheet, they suggested that it agreed well with fiber diffraction results from beta-keratin fibers. [2] However, since the alpha sheet did not appear to be energetically favorable, they argued that beta sheets would occur more commonly among normal proteins, [3] and subsequent demonstration that beta-keratin is made of beta sheets consigned the ...
An example of an amino acid sequence plotted on a helical wheel. Aliphatic residues are shown as blue squares, polar or negatively charged residues as red diamonds, and positively charged residues as black octagons. A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins.
The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.
The Simplified Molecular Input Line Entry System (SMILES) 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.
Protein primary structure is the linear sequence of amino acids in a peptide or protein. [1] By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the ...
A peptide hormone is a peptide that acts as a hormone. A proteose is a mixture of peptides produced by the hydrolysis of proteins. The term is somewhat archaic. A peptidergic agent (or drug) is a chemical which functions to directly modulate the peptide systems in the body or brain. An example is opioidergics, which are neuropeptidergics.
With the availability of high numbers of genomic sequences it becomes feasible to analyze such sequences for coevolving residues.The effectiveness of this approach results from the fact that a mutation in position i of a protein is more likely to be associated with a mutation in position j than with a back-mutation in i if both positions are functionally coupled (e.g. by taking part in an ...