In silico ADME/T modelling for rational drug design

Y Wang, J Xing, Y Xu, N Zhou, J Peng… - Quarterly reviews of …, 2015 - cambridge.org
In recent decades, in silico absorption, distribution, metabolism, excretion (ADME), and
toxicity (T) modelling as a tool for rational drug design has received considerable attention …

Rapid and Accurate Prediction of pKa Values of C–H Acids Using Graph Convolutional Neural Networks

R Roszak, W Beker, K Molga… - Journal of the American …, 2019 - ACS Publications
The ability to estimate the acidity of C–H groups within organic molecules in non-aqueous
solvents is important in synthetic planning to correctly predict which protons will be …

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

CM Ionescu, D Sehnal, FL Falginella, P Pant… - Journal of …, 2015 - Springer
Background Partial atomic charges are a well-established concept, useful in understanding
and modeling the chemical behavior of molecules, from simple compounds, to large …

High-quality and universal empirical atomic charges for chemoinformatics applications

S Geidl, T Bouchal, T Raček… - Journal of …, 2015 - Springer
Background Partial atomic charges describe the distribution of electron density in a
molecule and therefore provide clues to the chemical behaviour of molecules. Recently …

Efficient Assessment of 'Instantaneous pK' Values from Molecular Dynamics Simulations

P Duchstein, F Löffler, D Zahn - ChemPhysChem, 2024 - Wiley Online Library
We present a molecular simulation approach to studying the role of local and momentary
molecular environment for potential acid‐base reactions. For this, we combine …

Predicting pKa Values of Quinols and Related Aromatic Compounds with Multiple OH Groups

M Morency, S Néron, R Iftimie… - The Journal of Organic …, 2021 - ACS Publications
Quinonoid compounds play central roles as redox-active agents in photosynthesis and
respiration and are also promising replacements for inorganic materials currently used in …

Effect of the electronic properties of the side charges of neutral solvent molecules on the charges of the N and H atoms of the carbazole molecule: IR experiment and …

M Khodiev, N ISSAOUI, OM Al-Dossary… - Journal of Molecular …, 2024 - Elsevier
The IR spectral parameters of the absorption band of the valence vibration of the Nsingle
bondH bond of the carbazole molecule in several neutral solvents (n-hexane C 6 H 14 …

SAMPL6 challenge results from predictions based on a general Gaussian process model

CC Bannan, DL Mobley, AG Skillman - Journal of computer-aided …, 2018 - Springer
A variety of fields would benefit from accurate pK_a p K a predictions, especially drug design
due to the effect a change in ionization state can have on a molecule's physiochemical …

Probing the protonation and reduction of heptavalent neptunium with computational guidance

GC Benthin, H Rajapaksha, EL Markun… - Dalton …, 2024 - pubs.rsc.org
Influence of pH on the speciation and stability of heptavalent neptunium is poorly
understood although it is frequently invoked in the literature to explain experimental …

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method

CM Ionescu, S Geidl… - Journal of chemical …, 2013 - ACS Publications
We focused on the parametrization and evaluation of empirical models for fast and accurate
calculation of conformationally dependent atomic charges in proteins. The models were …