Elucidating solution structures of cyclic peptides using molecular dynamics simulations
Protein–protein interactions are vital to biological processes, but the shape and size of their
interfaces make them hard to target using small molecules. Cyclic peptides have shown …
interfaces make them hard to target using small molecules. Cyclic peptides have shown …
Conformational Control of Macrocycles by Remote Structural Modification: Focus Review
SD Appavoo, S Huh, DB Diaz, AK Yudin - Chemical reviews, 2019 - ACS Publications
The conformational analysis of macrocycles is a complex and challenging problem. There
are many factors that contribute to this complexity. These include a large number of degrees …
are many factors that contribute to this complexity. These include a large number of degrees …
[HTML][HTML] Applications of molecular dynamics simulation in structure prediction of peptides and proteins
H Geng, F Chen, J Ye, F Jiang - Computational and structural …, 2019 - Elsevier
Compared with rapid accumulation of protein sequences from high-throughput DNA
sequencing, obtaining experimental 3D structures of proteins is still much more difficult …
sequencing, obtaining experimental 3D structures of proteins is still much more difficult …
Enhanced sampling without borders: on global biasing functions and how to reweight them
Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of
biomolecular motions in atomistic resolution. However, the high computational demand of …
biomolecular motions in atomistic resolution. However, the high computational demand of …
Peptidic macrocycles-conformational sampling and thermodynamic characterization
Macrocycles are of considerable interest as highly specific drug candidates, yet they
challenge standard conformer generators with their large number of rotatable bonds and …
challenge standard conformer generators with their large number of rotatable bonds and …
Molecular dynamics simulations of cRGD-conjugated PEGylated TiO2 nanoparticles for targeted photodynamic therapy
The conjugation of high-affinity cRGD-containing peptides is a promising approach in
nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by …
nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by …
MacroConf–dataset & workflows to assess cyclic peptide solution structures
Knowing solution structures of cyclic peptides is essential for predicting pharmacokinetic
properties for drug discovery. Here, we report the MacroConf dataset along with …
properties for drug discovery. Here, we report the MacroConf dataset along with …
Insights into how cyclic peptides switch conformations
Cyclic peptides have recently emerged as promising modulators of protein–protein
interactions. However, it is currently highly difficult to predict the structures of cyclic peptides …
interactions. However, it is currently highly difficult to predict the structures of cyclic peptides …
Conformational restriction of peptides using dithiol bis-alkylation
L Peraro, TR Siegert, JA Kritzer - Methods in enzymology, 2016 - Elsevier
Macrocyclic peptides are highly promising as inhibitors of protein–protein interactions. While
many bond-forming reactions can be used to make cyclic peptides, most have limitations …
many bond-forming reactions can be used to make cyclic peptides, most have limitations …
Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α V β 3 by atomistic molecular dynamics and machine learning
Active targeting strategies have been proposed to enhance the selective uptake of
nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the …
nanoparticles (NPs) by diseased cells, and recent experimental findings have proven the …