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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 network of tertiary interactions, the possible spread of information within a protein can be investigated.
Protein identification is the process of assigning a name to a protein of interest (POI), based on its amino-acid sequence. Typically, only part of the protein’s sequence needs to be determined experimentally in order to identify the protein with reference to databases of protein sequences deduced from the DNA sequences of their genes.
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer.
A Janin plot generated by CING from chain A, Arginine residue number 18 in the protein Dynein Light Chain, (PDB ID 1y4o).The blue region show likely angle combinations for helical residues, while the yellow areas display regions that are common to strand-like stretches.
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
Protein topology is a property of protein molecule ... Knot theory which categorises chain entanglements. The usage of knot theory is limited to a small percentage of ...
Ramachandran plot - validate the torsion angles of a protein chain. Kleywegt plot - examine differences between the torsions of NCS-related chains. Incorrect chiral volumes - check for chiral centres with the wrong handedness. Unmodelled blobs - check for electron density not accounted for by existing atoms.