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  2. 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 ...

  3. Split-intein circular ligation of peptides and proteins

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

    As implemented there is also some constraint on the peptide sequence of the cyclic sequence; for example, libraries may use the sequence S GXX..XXP L to increase the efficiency of circularization of the peptide. [1] [2] SICLOPPS is frequently used with a library of randomized DNA sequence that permits the simultaneous production and screening ...

  4. 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 ...

  5. Macromolecular docking - Wikipedia

    en.wikipedia.org/wiki/Macromolecular_docking

    Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein –protein complexes are the most commonly attempted targets of such modelling, followed by protein– nucleic acid complexes.

  6. 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.

  7. Second messenger system - Wikipedia

    en.wikipedia.org/wiki/Second_messenger_system

    The mechanisms were worked out in detail by Martin Rodbell and Alfred G. Gilman, who won the 1994 Nobel Prize. [6] [7] Secondary messenger systems can be synthesized and activated by enzymes, for example, the cyclases that synthesize cyclic nucleotides, or by opening of ion channels to allow influx of metal ions, for example Ca 2+ signaling ...

  8. 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 ...

  9. Protein–ligand docking - Wikipedia

    en.wikipedia.org/wiki/Protein–ligand_docking

    Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide. Peptides are a highly flexible type of ligand that has proven to be a ...

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