Endogenous opiates and behavior: 2010

RJ Bodnar - Peptides, 2011 - Elsevier
This paper is the thirty-third consecutive installment of the annual review of research
concerning the endogenous opioid system. It summarizes papers published during 2010 …

PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations

PBPS Reis, D Vila-Vicosa, W Rocchia… - Journal of chemical …, 2020 - ACS Publications
The protonation of titratable residues has a significant impact on the structure and function of
biomolecules, influencing many physicochemical and ADME properties. Thus, the …

The impact of using single atomistic long-range cutoff schemes with the GROMOS 54A7 force field

TFD Silva, D Vila-Viçosa, PBPS Reis… - Journal of chemical …, 2018 - ACS Publications
With the recent increase in computing power, the molecular modeling community is now
more focused on improving the accuracy and overall quality of biomolecular simulations. For …

pKa Values of Titrable Amino Acids at the Water/Membrane Interface

VH Teixeira, D Vila-Viçosa, PBPS Reis… - Journal of Chemical …, 2016 - ACS Publications
Peptides and proteins protonation equilibrium is strongly influenced by its surrounding
media. Remarkably, until now, there have been no quantitative and systematic studies …

pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation

CAV Barreto, JNM Vitorino, PBPS Reis… - Journal of Chemical …, 2024 - ACS Publications
The increase in the available G protein-coupled receptor (GPCR) structures has been
pivotal in helping to understand their activation process. However, the role of protonation …

Delivery of analgesic peptides to the brain by nano-sized bolaamphiphilic vesicles made of monolayer membranes

M Popov, IA Hammad, T Bachar, S Grinberg… - European Journal of …, 2013 - Elsevier
Inefficient drug delivery to the brain is a major obstacle for pharmacological management of
brain diseases. We investigated the ability of bolavesicles–monolayer membrane vesicles …

Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

A Warshel, A Dryga - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
Electrostatic energies provide what is arguably the most effective tool for structure–function
correlation of biological molecules. Here, we provide an overview of the current state‐of‐the …

Constant-pH MD simulations of an oleic acid bilayer

D Vila-Vicosa, VH Teixeira, AM Baptista… - Journal of Chemical …, 2015 - ACS Publications
Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose
ionization and, consequently, intermolecular interactions are strongly dependent on the …

Protonation of dmpc in a bilayer environment using a linear response approximation

VH Teixeira, D Vila-Viçosa, AM Baptista… - Journal of Chemical …, 2014 - ACS Publications
pH is a very important property, influencing all important biomolecules such as proteins,
nucleic acids, and lipids. The effect of pH on proteins has been the subject of many …

MembIT–A Tool to Calculate Solute Membrane Insertions and Deformations in Molecular Dynamics Simulations

PMS Suzano, IDS Pires, TFD Silva… - Journal of …, 2023 - World Scientific
In molecular dynamics simulations of membrane systems, it is very important to evaluate the
interactions between membrane bilayers and other molecules like small compounds …