Self-assembly of peptides: The acceleration by molecular dynamics simulations and machine learning

N Cao, K Huang, J Xie, H Wang, X Shi - Nano Today, 2024 - Elsevier
Peptides, biopolymeric compounds connected by peptide bonds, have garnered significant
attention in recent years as their potential wide applications in fields such as drug delivery …

Antimicrobial peptide analogs from scorpions: Modifications and structure-activity

B Amorim-Carmo, AMS Parente, ES Souza… - Frontiers in Molecular …, 2022 - frontiersin.org
The rapid development of multidrug-resistant pathogens against conventional antibiotics is a
global public health problem. The irrational use of antibiotics has promoted therapeutic …

Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT …

G Colherinhas - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
In this work, we observe the behavior of the dipole moment, atomic charges, solute–solvent
interactions and NMR spectroscopy of aliphatic amino acids in a water solution via the …

Atomistic molecular dynamics study on the influence of high temperatures on the structure of peptide nanomembranes candidates for organic supercapacitor electrode

ED Alves, DX de Andrade, AR de Almeida… - Journal of Molecular …, 2021 - Elsevier
Recently, a series of organic structures formed by peptide self-assembly have been
reported, among which stand out the peptide nanomembranes with promising applications …

Hydroxylic, sulfur-containing and amidic amino acids in water solution: Atomic charges parameters for computational modeling using molecular dynamics simulation …

LBA Oliveira, WB Cardoso, G Colherinhas - Journal of Molecular Liquids, 2021 - Elsevier
In the present paper, we investigated the polarization effects on different amino acids (AAs)
structures, ie, Serine, Threonine, Cysteine, Methionine, Asparagine, and Glutamine. Initially …

Theoretical study of the absorption and emission spectra of 1, 2-Bis (9-anthryl) acetylene in cyclohexane and acetonitrile

V Manzoni, Y Orozco-Gonzalez, J Peon… - Chemical Physics …, 2023 - Elsevier
In this work we use TD-DFT combined with Polarizable Continuum Method and QM/MM
approach to analyze the absorption and emission spectra of 1, 2-bis (9-anthryl) acetylene in …

Molecular dynamics study of hydrogen bond in peptide membrane at 150–300 K

ED Alves, DX de Andrade, AR de Almeida… - Journal of Molecular …, 2022 - Elsevier
In this work, we develop molecular dynamics simulations to investigate the structural and
dynamic behavior of hydrogen bonds in A 6 X-type peptide structures (X= D, K, and R) in the …

Ultrasonic‐Assisted Biphasic Aqueous Extraction of Polyphenols from Vaccinium Dunalianum Leaves: Optimization, Antioxidant, and Tyrosinase Inhibition Activities

Y Yang, K Han, Z Liu, S Xie, J Xu, Y He… - Chemistry & …, 2024 - Wiley Online Library
To optimize the ultrasonic‐assisted biphasic aqueous extraction conditions for polyphenolic
compounds from Vaccinium dunalianum Wight leaves and investigate their antioxidant and …

Statistical and energetic analysis of hydrogen bonds in short and long peptide nanotapes/nanofibers using molecular dynamics simulations

AR de Almeida, DX de Andrade… - Journal of Molecular …, 2022 - Elsevier
In this work, we performed fully atomistic classical molecular dynamics simulations to
characterize the structural and energetic interaction of peptide nanoribbons/nanofibers with …

Polar zipper on a peptide nanomembrane: a characterization by potential of mean force

D X. de Andrade, G Colherinhas - The Journal of Physical …, 2022 - ACS Publications
In this work, nanomembranes formed by the I3 X GK (X= Q, S, or N) polar peptides are
studied to characterize the average force and energy required to separate two neighboring β …