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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 organisation of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure ...
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.
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.
Very close homologs (above 70% sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and ...
They consist of a long polypeptide chain that usually adopts a single stable three-dimensional structure. They fulfill a wide variety of functions including providing structural stability to cells, catalyze chemical reactions that produce or store energy or synthesize other biomolecules including nucleic acids and proteins, transport essential ...
Regarding the first duality (same symbol and name for gene or protein), the context usually makes the sense clear to scientific readers, and the nomenclatural systems also provide for some specificity by using italic for a symbol when the gene is meant and plain (roman) for when the protein is meant.
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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.
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