Accès ouvert
2026
preprint
OpenAlex
Niccolò Bruciaferri, Diogo Santos‐Martins, Matthew Holcomb, Manuel A. Llanos et autres
Water molecules in protein binding sites play a central role in ligand recognition by mediating stabilizing interactions and contributing desolvation penalties upon displacement. Reliable identification of hydration sites and quantification of their thermodynamic contributions remain challenging, as experimental water placement is often …
us
(code pays fourni par la source)
Accès ouvert
2026
dataset
OpenAlex
Stefano Forli, Niccolò Bruciaferri, Manuel A. Llanos
Dataset accompaininig the manuscript "MCSwell: Thermodynamic Characterization of Binding Site Hydration" Water placement set: predicted waters positions using conventional MD, WaterKit and MCSwell Thermodynamic profiling: thermodynamic properties calculated with MCSwell for a subset of the waters characterized with replica exchange thermodynamics integration …
us
(code pays fourni par la source)
Accès ouvert
2026
dataset
OpenAlex
Stefano Forli, Niccolò Bruciaferri, Manuel A. Llanos
Dataset accompaininig the manuscript "MCSwell: Thermodynamic Characterization of Binding Site Hydration" Water placement set: predicted waters positions using conventional MD, WaterKit and MCSwell Thermodynamic profiling: thermodynamic properties calculated with MCSwell for a subset of the waters characterized with replica exchange thermodynamics integration …
us
(code pays fourni par la source)
Accès ouvert
2025
article
OpenAlex
Diogo Santos‐Martins, Yiran He, Jérôme Eberhardt, Niccolò Bruciaferri et autres
Molecule parametrization is an essential requirement to guarantee the accuracy of docking calculations. Parametrization includes a proper perception of chemical properties such as bonds, formal charges and protonation states. This includes large biological macromolecules, such as proteins and nucleic acids, and small …
us
(code pays fourni par la source)
Accès ouvert
2025
preprint
OpenAlex
Diogo Santos‐Martins, Yiran He, Jérôme Eberhardt, Niccolò Bruciaferri et autres
Molecule parametrization is an essential requirement to guarantee the accuracy of simulations. Parametrization includes a proper perception of chemical properties such as bonds, formal charges and protonation states. This includes large biological macromolecules, such as proteins and nucleic acids, and small molecules, …
us
(code pays fourni par la source)
Accès ouvert
2024
article
OpenAlex
Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler et autres
Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including cryptic and allosteric pocket identification and pharmacophore profiling and supplement suites of …
us, ch
(code pays fourni par la source)
Accès ouvert
2024
preprint
OpenAlex
Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler et autres
Cosolvent molecular dynamics (MD) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including cryptic and allosteric pocket identification and pharmacophore profiling, and supplement suites of …
us, ch, in
(code pays fourni par la source)
Accès ouvert
2023
article
OpenAlex
Althea Hansel-Harris, Diogo Santos‐Martins, Niccolò Bruciaferri, Andreas F. Tillack et autres
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries in early stage drug discovery. As the size of compound libraries which can feasibly be screened grows, so do the challenges in result management …
us
(code pays fourni par la source)
Accès ouvert
2019
article
OpenAlex
Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli et autres
MOTIVATION: The correct localization of proteins in cell compartments is a key issue for their function. Particularly, mitochondrial proteins are physiologically active in different compartments and their aberrant localization contributes to the pathogenesis of human mitochondrial pathologies. Many computational methods exist to …
it
(code pays fourni par la source)