Peptidic macrocycles-conformational sampling and thermodynamic characterization

AS Kamenik, U Lessel, JE Fuchs, T Fox… - Journal of chemical …, 2018 - ACS Publications
Macrocycles are of considerable interest as highly specific drug candidates, yet they
challenge standard conformer generators with their large number of rotatable bonds and …

Integrating multiple accelerated molecular dynamics to improve accuracy of free energy calculations

X Peng, Y Zhang, Y Li, QL Liu, H Chu… - Journal of Chemical …, 2018 - ACS Publications
Accelerated Molecular Dynamics (aMD) is a promising enhanced sampling method to
explore the conformational space of biomolecules. However, the large statistical noise in …

From glucose to enantiopure morpholino β-amino acid: A new tool for stabilizing γ-turns in peptides

R Bucci, A Contini, F Clerici, S Pellegrino… - Organic Chemistry …, 2019 - pubs.rsc.org
A new cyclic enantiopure β-amino acid, named β-Morph, containing the morpholino ring,
was obtained in gram scale starting from an α-D-glucopyranose enantiopure material …

Prediction of accurate binding modes using combination of classical and accelerated molecular dynamics and free-energy perturbation calculations: an application to …

F Fratev, T Steinbrecher, SÓ Jónsdóttir - ACS omega, 2018 - ACS Publications
Estimating the correct binding modes of ligands in protein–ligand complexes is crucial not
only in the drug discovery process but also for elucidating potential toxicity mechanisms. In …

Accelerated molecular dynamics applied to the peptaibol folding problem

C Tyagi, T Marik, C Vágvölgyi, L Kredics… - International Journal of …, 2019 - mdpi.com
The use of enhanced sampling molecular dynamics simulations to facilitate the folding of
proteins is a relatively new approach which has quickly gained momentum in recent years …

Molecular Modeling of Chemosensory Protein 3 from Spodoptera litura and Its Binding Property with Plant Defensive Metabolites

S Singh, C Tyagi, IA Rather, JSM Sabir… - International Journal of …, 2020 - mdpi.com
Chemosensory perception in insects involves a broad set of chemosensory proteins (CSPs)
that identify the bouquet of chemical compounds present in the external environment and …

Quantitative assessment of molecular dynamics sampling for flexible systems

M Nemec, D Hoffmann - Journal of chemical theory and …, 2017 - ACS Publications
Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules
but at the same time is limited by the large size of the conformational space of these …

Localization of millisecond dynamics: dihedral entropy from accelerated MD

AS Kamenik, U Kahler, JE Fuchs… - Journal of Chemical …, 2016 - ACS Publications
Here, we demonstrate a method to capture local dynamics on a time scale 3 orders of
magnitude beyond state-of-the-art simulation approaches. We apply accelerated molecular …

Tripleurin XIIc: Peptide folding dynamics in aqueous and hydrophobic environment mimic using accelerated molecular dynamics

C Tyagi, T Marik, A Szekeres, C Vágvölgyi, L Kredics… - Molecules, 2019 - mdpi.com
Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-
terminal 1, 2-amino alcohol along with non-standard amino acid residues. New peptaibols …

Molecular dynamics simulation of tau peptides for the investigation of conformational changes induced by specific phosphorylation patterns

NS Gandhi, P Kukic, G Lippens, RL Mancera - Tau Protein: Methods and …, 2017 - Springer
The Tau protein plays an important role due to its biomolecular interactions in
neurodegenerative diseases. The lack of stable structure and various posttranslational …