138 citations · 467 across the 25 of their papers we have counts for
25 papers
A differentiable photon-by-photon likelihood for continuous free-energy landscapes and diffusion coefficients from single-molecule FRET
Lars Dingeldein, Roberto Covino
Single-molecule FRET probes the conformational dynamics of biomolecules by measuring the distance between two dyes. The experiment produces a stream of coloured photons, which is o…
Committors and Reaction Rates from Trial Functions That Violate the Boundary Conditions
Magnus Petersen, Simon Lichtinger, Roberto Covino
The committor is the optimal reaction coordinate for a rare transition: it pinpoints the transition state and fixes the rate, and it governs events from protein folding to crystal…
Accelerated descriptor-free path sampling for protein-ligand binding kinetics
Simon M. Lichtinger, Roberto Covino
The kinetics of protein-ligand binding systems are increasingly recognized as a key determinant of drug efficacy, yet remain far harder to compute than binding affinities. Existing…
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo +41
The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as…
A Machine-Learned Symbolic Committor for a Chemical Reaction: Retinal Isomerization
Kai Töpfer, Gianmarco Lazzeri, Vittoria Ossanna +4
The thermal cis-trans isomerization around the C=C double bond of retinal is a prototypical high-barrier reaction whose mechanism hinges on subtle out-of-plane bendin…
Quantitative and Predictive Folding Models from Limited Single-Molecule Data Using Simulation-Based Inference
Lars Dingeldein, Aaron Lyons, Pilar Cossio +2
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. How…
Understanding Reaction Mechanisms from Start to Finish
Rik S. Breebaart, Gianmarco Lazzeri, Roberto Covino +1
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from…
Follow the MEP: Scalable Neural Representations for Minimum-Energy Path Discovery in Molecular Systems
Magnus Petersen, Gemma Roig, Roberto Covino
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecula…
Cryo-em images are intrinsically low dimensional
Luke Evans, Octavian-Vlad Murad, Lars Dingeldein +3
Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via lea…
Optimal Rejection-Free Path Sampling
Gianmarco Lazzeri, Peter G. Bolhuis, Roberto Covino
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from…
Simulation-based inference of single-molecule experiments
Lars Dingeldein, Pilar Cossio, Roberto Covino
Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is…
Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations
Emil Jackel, Gianmarco Lazzeri, Roberto Covino
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for ex…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
Sampling a rare protein transition with a hybrid classical-quantum computing algorithm
Danial Ghamari, Roberto Covino, Pietro Faccioli
Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time i…
Molecular free energies, rates, and mechanisms from data-efficient path sampling simulations
Gianmarco Lazzeri, Hendrik Jung, Peter G. Bolhuis +1
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scale…
Simulation-based inference of single-molecule force spectroscopy
Lars Dingeldein, Pilar Cossio, Roberto Covino
Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular self-organization. However, the coupling of the molecule with the ever-present experimental d…
Information-theoretical measures identify accurate low-resolution representations of protein configurational space
Margherita Mele, Roberto Covino, Raffaello Potestio
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity…
Sampling Rare Conformational Transitions with a Quantum Computer
Danial Ghamari, Philipp Hauke, Roberto Covino +1
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Mo…
Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments
Hendrik Jung, Roberto Covino, A Arjun +2
Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mech…
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors
Roberto Covino, Michael T. Woodside, Gerhard Hummer +2
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monit…
Artificial Intelligence Assists Discovery of Reaction Coordinates and Mechanisms from Molecular Dynamics Simulations
Hendrik Jung, Roberto Covino, Gerhard Hummer
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computati…
iMapD: intrinsic Map Dynamics exploration for uncharted effective free energy landscapes
Eliodoro Chiavazzo, Ronald R. Coifman, Roberto Covino +4
We describe and implement iMapD, a computer-assisted approach for accelerating the exploration of uncharted effective Free Energy Surfaces (FES), and more generally for the extract…
Identification and Analysis of Transition and Metastable Markov States
Linda Martini, Adam Kells, Gerhard Hummer +2
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD…
Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
Silvio a Beccara, Tatjana Skrbic, Roberto Covino +2
We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported ef…