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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 ...
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 ...
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.
Backbone-dependent rotamer library for serine.Each plot shows the population of the χ 1 rotamers of serine as a function of the backbone dihedral angles φ and ψ. In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations (known as rotamers) of the amino acid side chains in proteins as a function ...
The first and third scales are derived from the physiochemical properties of the amino acid side chains. These scales result mainly from inspection of the amino acid structures. [14] [1] Biswas et al., divided the scales based on the method used to obtain the scale into five different categories. [3]
For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left. A Ramachandran plot generated from human PCNA, a trimeric DNA clamp protein that contains both β-sheet and α-helix (PDB ID 1AXC). The red, brown, and yellow regions represent the favored ...
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.
A conservative replacement (also called a conservative mutation or a conservative substitution or a homologous replacement) is an amino acid replacement in a protein that changes a given amino acid to a different amino acid with similar biochemical properties (e.g. charge, hydrophobicity and size). [1] [2]