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  2. Split-intein circular ligation of peptides and proteins

    en.wikipedia.org/wiki/Split-intein_circular...

    A number of natural antimicrobial peptides are cyclic, and the products of SICLOPPS are "increasingly viewed as ideal backbones for modulation of protein-protein interactions." [3] Circular peptides tend to be resistant to protease activity, and may be suitable for use as orally administered drugs.

  3. Cyclic peptide - Wikipedia

    en.wikipedia.org/wiki/Cyclic_peptide

    α-Amanitin Bacitracin Ciclosporin. Cyclic peptides are polypeptide chains which contain a circular sequence of bonds. [1] This can be through a connection between the amino and carboxyl ends of the peptide, for example in cyclosporin; a connection between the amino end and a side chain, for example in bacitracin; the carboxyl end and a side chain, for example in colistin; or two side chains ...

  4. Arginylglycylaspartic acid - Wikipedia

    en.wikipedia.org/wiki/Arginylglycylaspartic_acid

    The structural rigidity of cyclic RGD peptides improves their binding properties and prevents degradation at the highly susceptible aspartic acid residue, thereby increasing their stability. [30] Many RGD derivative drugs and diagnostics are cyclized, including Eptifibatide, Cilengitide, CEND-1, and 18 F-Galacto-RGD, and 18 F-Fluciclatide-RGD.

  5. Docking (molecular) - Wikipedia

    en.wikipedia.org/wiki/Docking_(molecular)

    Docking flow-chart overview. To perform a docking screen, the first requirement is a structure of the protein of interest. Usually the structure has been determined using a biophysical technique such as X-ray crystallography, NMR spectroscopy or; cryo-electron microscopy (cryo-EM), but can also derive from homology modeling construction. This ...

  6. Circular permutation in proteins - Wikipedia

    en.wikipedia.org/wiki/Circular_permutation_in...

    After determining the peptide sequence of the lectin protein favin, they noticed its similarity to a known protein – concanavalin A – except that the ends were circularly permuted. Later work confirmed the circular permutation between the pair [ 2 ] and showed that concanavalin A is permuted post-translationally [ 3 ] through cleavage and ...

  7. Protein–ligand docking - Wikipedia

    en.wikipedia.org/wiki/Protein–ligand_docking

    Coarse-grained models are often implemented in the case of protein-peptide docking, as they frequently involve large-scale conformation transitions of the protein receptor. [7] [8] AutoDock is one of the computational tools frequently used to model the interactions between proteins and ligands during the drug discovery process. Although the ...

  8. Diketopiperazine - Wikipedia

    en.wikipedia.org/wiki/Diketopiperazine

    DKP's are the smallest known class of cyclic peptide. [1] Despite their name, they are not ketones, but amides. Three regioisomers are possible, differing in the locations of the carbonyl groups. Retosiban [2] is a diketopiperazine being investigated as an oral drug. One isomer is an oxamide obtained from ethylenediamine.

  9. Searching the conformational space for docking - Wikipedia

    en.wikipedia.org/wiki/Searching_the...

    The most common technique used in many docking programs, shape-complementarity methods focus on the match between the receptor and the ligand in order to find an optimal pose. Programs include DOCK, [3] FRED, [4] GLIDE, [5] SURFLEX, [6] eHiTS [7] and many more. Most methods describe the molecules in terms of a finite number of descriptors that ...