Insights into protein–ligand interactions: mechanisms, models, and methods

X Du, Y Li, YL Xia, SM Ai, J Liang, P Sang… - International journal of …, 2016 - mdpi.com
Molecular recognition, which is the process of biological macromolecules interacting with
each other or various small molecules with a high specificity and affinity to form a specific …

How water's properties are encoded in its molecular structure and energies

E Brini, CJ Fennell, M Fernandez-Serra… - Chemical …, 2017 - ACS Publications
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …

Binding affinity via docking: fact and fiction

T Pantsar, A Poso - Molecules, 2018 - mdpi.com
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to
Macromolecule-Ligand Interactions”, where they described a method “to explore …

Role of molecular dynamics and related methods in drug discovery

M De Vivo, M Masetti, G Bottegoni… - Journal of medicinal …, 2016 - ACS Publications
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Alchemical binding free energy calculations in AMBER20: Advances and best practices for drug discovery

TS Lee, BK Allen, TJ Giese, Z Guo, P Li… - Journal of Chemical …, 2020 - ACS Publications
Predicting protein–ligand binding affinities and the associated thermodynamics of
biomolecular recognition is a primary objective of structure-based drug design. Alchemical …

Water is an active matrix of life for cell and molecular biology

P Ball - Proceedings of the National Academy of Sciences, 2017 - National Acad Sciences
Szent-Győrgi called water the “matrix of life” and claimed that there was no life without it.
This statement is true, as far as we know, on our planet, but it is not clear whether it must …

Experimental binding energies in supramolecular complexes

F Biedermann, HJ Schneider - Chemical reviews, 2016 - ACS Publications
On the basis of many literature measurements, a critical overview is given on essential
noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses …

Molecular recognition in chemical and biological systems

E Persch, O Dumele, F Diederich - … Chemie International Edition, 2015 - Wiley Online Library
Abstract Structure‐based ligand design in medicinal chemistry and crop protection relies on
the identification and quantification of weak noncovalent interactions and understanding the …

The hydrophobic effect revisited—studies with supramolecular complexes imply high‐energy water as a noncovalent driving force

F Biedermann, WM Nau… - Angewandte Chemie …, 2014 - Wiley Online Library
Traditional descriptions of the hydrophobic effect on the basis of entropic arguments or the
calculation of solvent‐occupied surfaces must be questioned in view of new results obtained …

Catalase and its mysteries

HS Tehrani, AA Moosavi-Movahedi - Progress in biophysics and molecular …, 2018 - Elsevier
Catalase is one of the firsts in every realm of biological sciences. At the same time it also has
a number of unusual features. It has one of the highest turnover numbers of all enzymes. It is …