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Lin and her lab use computational chemistry to provide information on the solution structures of cyclic peptides. [2] They recently successfully used molecular dynamics simulation with enhanced sampling methods to design well-structured cyclic peptides. [12] [13]
Using molecular dynamics simulation, the team is able to measure the contact angle of water nanodroplet on the planar networks (caHydrophobicity). On the other hand, previous studies show that the minimum of excess chemical potential of a hard-sphere solute with respect to that in the bulk exhibits a linear dependence on cosine value of contact ...
Present in nature are both linear and cyclic tetrapeptides (CTPs), the latter of which mimics protein reverse turns which are often present on the surface of proteins and druggable targets. [ 1 ] [ 2 ] Tetrapeptides may be cyclized by a fourth peptide bond or other covalent bonds .
Pentapeptide repeats were initially predicted from sequence to possess a right handed beta helix with three sides. [3] The first crystal structure of a pentapeptide repeat protein was the MfpA protein solved by Hegde and colleagues.
Figure 1. Flow Chart of Virtual Screening [1]. Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
The macrocyclic effect is the high affinity of metal cations for macrocyclic ligands, compared to their acyclic analogues. [7] [8] The high affinity of macrocyclic ligands is thought to be a combination of the entropic effect seen in the chelate effect, together with an additional energetic contribution that comes from the preorganized nature of the ligating groups (that is, no additional ...
Nodularin-R is the predominant toxin variant, though 10 variants of nodularin have been discovered to date. Nodularins are cyclic nonribosomal pentapeptides and contain several unusual non-proteinogenic amino acids such as N-methyl-didehydroaminobutyric acid and the β-amino acid ADDA. These compounds are relatively stable compounds: light ...