Binding of small-molecule ligands to proteins:“what you see” is not always “what you get”

DL Mobley, KA Dill - Structure, 2009 - cell.com
We review insights from computational studies of affinities of ligands binding to proteins. The
power of structural biology is in translating knowledge of protein structures into insights …

An NMR perspective on enzyme dynamics

DD Boehr, HJ Dyson, PE Wright - Chemical reviews, 2006 - ACS Publications
Enzyme catalysis is an inherently dynamic process. Binding and release of ligands is often
accompanied by conformational changes, both subtle and dramatic (reviewed more …

Ligand binding remodels protein side-chain conformational heterogeneity

SA Wankowicz, SH de Oliveira, DW Hogan… - Elife, 2022 - elifesciences.org
While protein conformational heterogeneity plays an important role in many aspects of
biological function, including ligand binding, its impact has been difficult to quantify …

[图书][B] Introduction to proteins: structure, function, and motion

A Kessel, N Ben-Tal - 2018 - taylorfrancis.com
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

Target flexibility: an emerging consideration in drug discovery and design

P Cozzini, GE Kellogg, F Spyrakis… - Journal of medicinal …, 2008 - ACS Publications
Structure-based drug discovery has played an important role in medicinal chemistry, 1
beginning nearly when the first X-ray crystal structure of the myoglobin and hemoglobin …

Understanding nature's catalytic toolkit

A Gutteridge, JM Thornton - Trends in biochemical sciences, 2005 - cell.com
Enzymes catalyse numerous reactions in nature, often causing spectacular accelerations in
the catalysis rate. One aspect of understanding how enzymes achieve these feats is to …

Insights into protein flexibility: the relationship between normal modes and conformational change upon protein–protein docking

SE Dobbins, VI Lesk… - Proceedings of the …, 2008 - National Acad Sciences
Understanding protein interactions has broad implications for the mechanism of recognition,
protein design, and assigning putative functions to uncharacterized proteins. Studying …

Potential and limitations of ensemble docking

O Korb, TSG Olsson, SJ Bowden, RJ Hall… - Journal of chemical …, 2012 - ACS Publications
A major problem in structure-based virtual screening applications is the appropriate
selection of a single or even multiple protein structures to be used in the virtual screening …

Role of computational methods in going beyond X-ray crystallography to explore protein structure and dynamics

A Srivastava, T Nagai, A Srivastava… - International journal of …, 2018 - mdpi.com
Protein structural biology came a long way since the determination of the first three-
dimensional structure of myoglobin about six decades ago. Across this period, X-ray …

Post-translational modifications induce significant yet not extreme changes to protein structure

F Xin, P Radivojac - Bioinformatics, 2012 - academic.oup.com
Motivation: A number of studies of individual proteins have shown that post-translational
modifications (PTMs) are associated with structural rearrangements of their target proteins …