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  2. Protein secondary structure - Wikipedia

    en.wikipedia.org/wiki/Protein_secondary_structure

    The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined ...

  3. Beta sheet - Wikipedia

    en.wikipedia.org/wiki/Beta_sheet

    The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands ( β-strands ) connected laterally by at least two or three backbone hydrogen bonds , forming a generally twisted, pleated sheet.

  4. Ribbon diagram - Wikipedia

    en.wikipedia.org/wiki/Ribbon_diagram

    Ribbon diagram of myoglobin bound to haem (sticks) and oxygen (red spheres) (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 ...

  5. Biomolecular structure - Wikipedia

    en.wikipedia.org/wiki/Biomolecular_structure

    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 ...

  6. Turn (biochemistry) - Wikipedia

    en.wikipedia.org/wiki/Turn_(biochemistry)

    A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. For example, a beta hairpin connects two hydrogen-bonded , antiparallel β-strands (a rather confusing name, since a β-hairpin may contain many types of turns – α, β, γ, etc.).

  7. DSSP (algorithm) - Wikipedia

    en.wikipedia.org/wiki/DSSP_(algorithm)

    The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, [2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.

  8. GOR method - Wikipedia

    en.wikipedia.org/wiki/GOR_method

    The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17 ...

  9. Alpha sheet - Wikipedia

    en.wikipedia.org/wiki/Alpha_sheet

    Although the alpha sheet is only rarely observed in natural protein structures, it has been speculated to play a role in amyloid disease [4] and it was found to be a stable form for amyloidogenic proteins in molecular dynamics simulations. [5] [6] Alpha sheets have also been observed in X-ray crystallography structures of designed peptides. [4]