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  2. Protein contact map - Wikipedia

    en.wikipedia.org/wiki/Protein_contact_map

    A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i {\displaystyle i} and j {\displaystyle j} , the i j {\displaystyle ij} element of the matrix is 1 if the two residues are closer than a predetermined ...

  3. Protein structure - Wikipedia

    en.wikipedia.org/wiki/Protein_structure

    A structural domain is an element of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins.

  4. 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.).

  5. Protein primary structure - Wikipedia

    en.wikipedia.org/wiki/Protein_primary_structure

    Protein primary structure is the linear sequence of amino acids in a peptide or protein. [1] By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the ...

  6. Alpha helix - Wikipedia

    en.wikipedia.org/wiki/Alpha_helix

    The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)

  7. 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).

  8. Structural alignment - Wikipedia

    en.wikipedia.org/wiki/Structural_alignment

    The matrix increases in dimensionality as the number of structures to be simultaneously aligned increases. Reducing the protein to a coarse metric such as secondary structure elements (SSEs) or structural fragments can also produce sensible alignments, despite the loss of information from discarding distances, as noise is also discarded. [20]

  9. Plastocyanin - Wikipedia

    en.wikipedia.org/wiki/Plastocyanin

    Plastocyanin is a copper-containing protein that mediates electron-transfer. It is found in a variety of plants, where it participates in photosynthesis. The protein is a prototype of the blue copper proteins, a family of intensely blue-colored metalloproteins. Specifically, it falls into the group of small type I blue copper proteins called ...

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