62 citations · 279 across the 15 of their papers we have counts for
5 papers · 1 filter
Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics
Riccardo Capelli, Paolo Carloni, Michele Parrinello
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics…
Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme
Thomas Tarenzi, Vania Calandrini, Raffaello Potestio +2
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the re…
Statistical Analysis of -Holes: A Novel Complementary View on Halogen Bonding
Michal H. Kolář, Paolo Carloni, Pavel Hobza
To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were…
Proton Dynamics in Protein Mass Spectrometry
Jinyu Li, Wenping Lyu, Giulia Rossetti +7
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of p…
Many-Body meets QM/MM: Application to indole in water solution
Adriano Mosca Conte, Emiliano Ippoliti, Rodolfo Del Sole +2
Spectral properties of chromophores are used to probe complex biological processes in vitro and in vivo, yet how the environment tunes their optical properties is far from being fu…