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 …
Steering new drug discovery campaigns: permeability, solubility, and physicochemical properties in the bRo5 chemical space
An increasing number of drug discovery programs concern compounds in the beyond rule of
5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent …
5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent …
Structure prediction of cyclic peptides by molecular dynamics+ machine learning
Recent computational methods have made strides in discovering well-structured cyclic
peptides that preferentially populate a single conformation. However, many successful cyclic …
peptides that preferentially populate a single conformation. However, many successful cyclic …
Conformation and permeability: cyclic hexapeptide diastereomers
S Ono, MR Naylor, CE Townsend… - Journal of chemical …, 2019 - ACS Publications
Conformational ensembles of eight cyclic hexapeptide diastereomers in explicit
cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics …
cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics …
Native and Engineered Cyclic Disulfide-Rich Peptides as Drug Leads
Bioactive peptides are a highly abundant and diverse group of molecules that exhibit a wide
range of structural and functional variation. Despite their immense therapeutic potential …
range of structural and functional variation. Despite their immense therapeutic potential …
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 …
Understanding ring puckering in small molecules and cyclic peptides
The geometry of a molecule plays a significant role in determining its physical and chemical
properties. Despite its importance, there are relatively few studies on ring puckering and …
properties. Despite its importance, there are relatively few studies on ring puckering and …
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 …