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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 ...
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.
Knowledge of the relationship between a protein's structure and its dynamic behavior is essential for understanding protein function. The description of a protein three dimensional structure as a network of hydrogen bonding interactions (HB plot) [12] was introduced as a tool for exploring protein structure and function. By analyzing the ...
describe the coordinates of the atoms that are part of the protein. For example, the first ATOM line above describes the alpha-N atom of the first residue of peptide chain A, which is a proline residue; the first three floating point numbers are its x, y and z coordinates and are in units of Ångströms. [7]
Knowing the structure of a similar homologous sequence (for example a member of the same protein family) allows highly accurate prediction of the tertiary structure by homology modeling. If the full-length protein sequence is available, it is possible to estimate its general biophysical properties, such as its isoelectric point.
Draw the structure, and save it as a ChemDraw file. If you drew the structure before applying any settings, then you need to select the object, open the “Object” menu and choose “Apply document settings from → ACS Document 1996”. Then save it as a PNG file, to be read by an image editor such as GIMP or IrfanView (see below for details).
The primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry).For a typical unbranched, un-crosslinked biopolymer (such as a molecule of a typical intracellular protein, or of DNA or RNA), the primary structure is equivalent to specifying the sequence of its monomeric subunits, such as amino ...
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.