Publications by Stefano Vanni | EPFL Graph Search

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The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

This thesis is devoted to the study of the activation mechanism of G-protein coupled receptors (GPCRs), one of the largest and most diverse protein families in mammalian genomes, by means of different computer-based simulation techniques. Using force field ...

The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of be ...

G protein coupled receptors (GPCRs) are a large eukaryotic protein family of transmembrane receptors that react to a signal coming from the extracellular environment to generate an intracellular response through the activation of a signal transduction path ...

Recently, a 3.65 angstrom resolution structure of the transporter, NorM from the multidrug and toxic compound extrusion family has been determined in the outward-facing conformation. This antiporter uses electrochemical gradients to drive substrate export ...

Many G protein-coupled receptors (GPCRs) are known to form dimers or even oligomers, and these aggregated states have been proposed as functional units responsible for signal transduction and G protein activation. However, the nature of their involvement h ...

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one corresp ...

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Stefano Vanni

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Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

A conserved protonation-induced switch can trigger "ionic lock" formation in adrenergic receptors

A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations

Ion Binding and Internal Hydration in the Multidrug Resistance Secondary Active Transporter NorM Investigated by Molecular Dynamics Simulations

Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild-Type Beta1 and Beta2 Adrenergic Receptors

Role of Aggregation in Rhodopsin Signal Transduction

Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Identification of clustering artifacts in photoactivated localization microscopy