Ligand binding free energy and kinetics calculation in 2020
V Limongelli - Wiley Interdisciplinary Reviews: Computational …, 2020 - Wiley Online Library
Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the
advent of computers, many scientists have put efforts in developing theoretical models that …
advent of computers, many scientists have put efforts in developing theoretical models that …
Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities
Abstract γ-Aminobutyric acid type A (GABAA) receptors are pentameric ligand-gated ion
channels abundant in the central nervous system and are prolific drug targets for treating …
channels abundant in the central nervous system and are prolific drug targets for treating …
Ligand binding free-energy calculations with funnel metadynamics
S Raniolo, V Limongelli - Nature Protocols, 2020 - nature.com
The accurate resolution of the binding mechanism of a ligand to its molecular target is
fundamental to develop a successful drug design campaign. Free-energy calculations …
fundamental to develop a successful drug design campaign. Free-energy calculations …
Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions
of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell …
of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell …
Conformational changes in the epidermal growth factor receptor: role of the transmembrane domain investigated by coarse-grained metadynamics free energy …
M Lelimousin, V Limongelli… - Journal of the American …, 2016 - ACS Publications
The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates
key aspects of cellular function. Activation of the EGFR is linked to changes in the …
key aspects of cellular function. Activation of the EGFR is linked to changes in the …
Accelerating the calculation of protein–ligand binding free energy and residence times using dynamically optimized collective variables
ZF Brotzakis, V Limongelli… - Journal of chemical theory …, 2018 - ACS Publications
Elucidation of the ligand/protein binding interaction is of paramount relevance in
pharmacology to increase the success rate of drug design. To this end, a number of …
pharmacology to increase the success rate of drug design. To this end, a number of …
Ligand binding, unbinding, and allosteric effects: deciphering small-molecule modulation of HSP90
The molecular chaperone HSP90 oversees the functional activation of a large number of
client proteins. Because of its role in multiple pathways linked to cancer and …
client proteins. Because of its role in multiple pathways linked to cancer and …
Computational methods and theory for ion channel research
Ion channels are fundamental biological devices that act as gates in order to ensure
selective ion transport across cellular membranes; their operation constitutes the molecular …
selective ion transport across cellular membranes; their operation constitutes the molecular …
Exploring cryptic pockets formation in targets of pharmaceutical interest with SWISH
F Comitani, FL Gervasio - Journal of chemical theory and …, 2018 - ACS Publications
Cryptic (hidden) pockets are sites that are not visible on unliganded target proteins'
structures and only become apparent when a ligand binds. They might provide a valid …
structures and only become apparent when a ligand binds. They might provide a valid …
Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles
Inorganic nanoparticles show promising properties that allow them to be efficiently used as
drug carriers. The main limitation in this type of application is currently the drug loading …
drug carriers. The main limitation in this type of application is currently the drug loading …