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  2. Protein contact map - Wikipedia

    en.wikipedia.org/wiki/Protein_contact_map

    With the availability of high numbers of genomic sequences it becomes feasible to analyze such sequences for coevolving residues.The effectiveness of this approach results from the fact that a mutation in position i of a protein is more likely to be associated with a mutation in position j than with a back-mutation in i if both positions are functionally coupled (e.g. by taking part in an ...

  3. Hierarchical editing language for macromolecules - Wikipedia

    en.wikipedia.org/wiki/Hierarchical_Editing...

    It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers. [1] HELM was developed by a consortium of pharmaceutical companies in what is known as the Pistoia Alliance. Development began in 2008. In 2012 the notation was published openly and for ...

  4. Protein secondary structure - Wikipedia

    en.wikipedia.org/wiki/Protein_secondary_structure

    The image above contains clickable links This diagram (which is interactive) of protein structure uses PCNA as an example. ( PDB : 1AXC ) Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. [ 1 ]

  5. Ribosomally synthesized and post-translationally modified ...

    en.wikipedia.org/wiki/Ribosomally_synthesized...

    RiPPs consist of any peptides (i.e. molecular weight below 10 kDa) that are ribosomally-produced and undergo some degree of enzymatic post-translational modification.This combination of peptide translation and modification is referred to as "post-ribosomal peptide synthesis" (PRPS) in analogy with nonribosomal peptide synthesis (NRPS).

  6. Turn (biochemistry) - Wikipedia

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

    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.). Beta hairpins may be classified according to the number of residues that make up the turn - that is, that are not part of the flanking β-strands. [ 7 ]

  7. Ramachandran plot - Wikipedia

    en.wikipedia.org/wiki/Ramachandran_plot

    The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. [3] The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and ...

  8. Peptidomimetic - Wikipedia

    en.wikipedia.org/wiki/Peptidomimetic

    Figure 1. Classification of peptidomimetics. [1]A peptidomimetic is a small protein-like chain designed to mimic a peptide. [1] [2] They typically arise either from modification of an existing peptide, or by designing similar systems that mimic peptides, such as peptoids and β-peptides.

  9. Stapled peptide - Wikipedia

    en.wikipedia.org/wiki/Stapled_peptide

    A stapled peptide is a modified peptide (class A peptidomimetic), typically in an alpha-helical conformation, [2] that is constrained by a synthetic brace ("staple"). [3] The staple is formed by a covalent linkage between two amino acid side-chains, forming a peptide macrocycle. Staples, generally speaking, refer to a covalent linkage of two ...