Hydrogen-bond donors in drug design

PW Kenny - Journal of Medicinal Chemistry, 2022 - ACS Publications
Hydrogen-bond donors are seen to cause more problems for drug designers than hydrogen-
bond acceptors. Most of the polarity in drug-like compounds comes from hydrogen-bond …

GalaxyWater-CNN: Prediction of water positions on the protein structure by a 3D-convolutional neural network

S Park, C Seok - Journal of Chemical Information and Modeling, 2022 - ACS Publications
Proteins interact with numerous water molecules to perform their physiological functions in
biological organisms. Most water molecules act as solvent media; hence, their roles may be …

Distribution and function of glycosaminoglycans and proteoglycans in the development, homeostasis and pathology of the ocular surface

S Puri, YM Coulson-Thomas, TF Gesteira… - Frontiers in cell and …, 2020 - frontiersin.org
The ocular surface, which forms the interface between the eye and the external environment,
includes the cornea, corneoscleral limbus, the conjunctiva and the accessory glands that …

Advances in the discovery of new chemotypes through ultra-large library docking

F Potlitz, A Link, L Schulig - Expert opinion on drug discovery, 2023 - Taylor & Francis
Introduction The size and complexity of virtual screening libraries in drug discovery have
skyrocketed in recent years, reaching up to multiple billions of accessible compounds …

Solvation free energy as a measure of hydrophobicity: application to serine protease binding interfaces

J Kraml, AS Kamenik, F Waibl… - Journal of chemical …, 2019 - ACS Publications
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In
substrate binding, but also in structure-based drug design, the thermodynamic properties of …

Spatially resolved hydration thermodynamics in biomolecular systems

S Mukherjee, LV Schäfer - The Journal of Physical Chemistry B, 2022 - ACS Publications
Water is essential for the structure, dynamics, energetics, and thus the function of
biomolecules. It is a formidable challenge to elicit, in microscopic detail, the role of the …

Hydration free energies and solvation structures with molecular density functional theory in the hypernetted chain approximation

S Luukkonen, M Levesque, L Belloni… - The Journal of Chemical …, 2020 - pubs.aip.org
The capability of molecular density functional theory in its lowest, second-order
approximation, equivalent to the hypernetted chain approximation in integral equations, to …

Total free energy analysis of fully hydrated proteins

J Kalayan, A Chakravorty, J Warwicker… - Proteins: Structure …, 2023 - Wiley Online Library
The total free energy of a hydrated biomolecule and its corresponding decomposition of
energy and entropy provides detailed information about regions of thermodynamic stability …

Simple parameter-free bridge functionals for molecular density functional theory. Application to hydrophobic solvation

D Borgis, S Luukkonen, L Belloni… - The Journal of Physical …, 2020 - ACS Publications
Computer simulations have been fundamental in understanding the fine details of
hydrophobic solvation and hydrophobic interactions. Alternative approaches based on liquid …

Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

D Roy, A Kovalenko - International Journal of Molecular Sciences, 2021 - mdpi.com
The statistical mechanics-based 3-dimensional reference interaction site model with the
Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an …