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Once a cyclic peptide is identified with a biological activity of interest, it may also be possible to identify the target of the peptide (a gene that encodes a protein with which it interacts) by functional complementation, facilitating a better understanding of its mechanism of action.
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 ...
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 ...
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.
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 ...
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 ...
Docking glossary Receptor or host or lock The "receiving" molecule, most commonly a protein or other biopolymer. Ligand or guest or key The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer. Docking Computational simulation of a candidate ligand binding to a ...
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 ...