Jonathan Barnoud
YOU?
Author Swipe
View article: Author response: Martinize2 and Vermouth provide a unified framework for molecular topology generation
Author response: Martinize2 and Vermouth provide a unified framework for molecular topology generation Open
View article: NanoVer Server: A Python Package for Serving Real-Time Multi-User Interactive Molecular Dynamics in Virtual Reality
NanoVer Server: A Python Package for Serving Real-Time Multi-User Interactive Molecular Dynamics in Virtual Reality Open
View article: Author response: Martinize2 and Vermouth: Unified Framework for Topology Generation
Author response: Martinize2 and Vermouth: Unified Framework for Topology Generation Open
View article: Martinize2 and Vermouth: Unified Framework for Topology Generation
Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems
AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems Open
Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their utili…
View article: Reviewer #3 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation
Reviewer #3 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Reviewer #2 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation
Reviewer #2 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Reviewer #1 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation
Reviewer #1 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Martinize2 and Vermouth: Unified Framework for Topology Generation
Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Author response: Martinize2 and Vermouth: Unified Framework for Topology Generation
Author response: Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Measuring the Limit of Perception of Bond Stiffness of Interactive Molecules in VR via a Gamified Psychophysics Experiment
Measuring the Limit of Perception of Bond Stiffness of Interactive Molecules in VR via a Gamified Psychophysics Experiment Open
View article: Martini 3 Coarse-Grained Force Field for Cholesterol
Martini 3 Coarse-Grained Force Field for Cholesterol Open
Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improve…
View article: Free energy along drug-protein binding pathways interactively sampled in virtual reality
Free energy along drug-protein binding pathways interactively sampled in virtual reality Open
View article: Martini 3 Coarse-Grained Force Field for cholesterol
Martini 3 Coarse-Grained Force Field for cholesterol Open
Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvem…
View article: Reviewer #2 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation
Reviewer #2 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Martinize2 and Vermouth: Unified Framework for Topology Generation
Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Reviewer #1 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation
Reviewer #1 (Public Review): Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Martinize2 and Vermouth provide a unified framework for molecular topology generation
Martinize2 and Vermouth provide a unified framework for molecular topology generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Martini 3 Coarse-Grained Force Field for cholesterol
Martini 3 Coarse-Grained Force Field for cholesterol Open
Cholesterol plays a crucial role in biomembranes by regulating various properties such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvem…
View article: Building a community-driven ecosystem for fast, reproducible, and reusable molecular simulation analysis using mdanalysis
Building a community-driven ecosystem for fast, reproducible, and reusable molecular simulation analysis using mdanalysis Open
View article: MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis
MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis Open
The reproducibility and transparency of scientific findings are widely recognized as crucial for promoting scientific progress. However, when it comes to scientific software, researchers face many barriers and few incentives to ensure that…
View article: Martinize2 and Vermouth: Unified Framework for Topology Generation
Martinize2 and Vermouth: Unified Framework for Topology Generation Open
Ongoing advances in force field and computer hardware development enable the use of molecular dynamics (MD) to simulate increasingly complex systems with the ultimate goal of reaching cellular complexity. At the same time, rational design …
View article: Free energy for drug-protein binding from human-guided atomistic simulations in virtual reality - Supplementary Files
Free energy for drug-protein binding from human-guided atomistic simulations in virtual reality - Supplementary Files Open
iMD-VR trajectories, narupa inputs, system parameters, and umbrella sampling data.
View article: The emerging potential of interactive virtual reality in drug discovery
The emerging potential of interactive virtual reality in drug discovery Open
The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together i…
View article: Virtual reality sampled pathways guide free energy calculation of protein-ligand binding
Virtual reality sampled pathways guide free energy calculation of protein-ligand binding Open
We describe a novel two-step approach for combining cloud-mounted interactive molecular dynamics in virtual reality (iMD-VR) with free energy sampling (FES) approaches to quantitatively explore the dynamics of biological processes at the m…
View article: Interactivity: the missing link between virtual reality technology and drug discovery pipelines
Interactivity: the missing link between virtual reality technology and drug discovery pipelines Open
The potential of virtual reality (VR) to contribute to drug design and development has been recognised for many years. Hardware and software developments now mean that this potential is beginning to be realised, and VR methods are being ac…
View article: Martini 3 Coarse‐Grained Force Field: Small Molecules
Martini 3 Coarse‐Grained Force Field: Small Molecules Open
The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. Here, we describe how small molecule…
View article: Martini 3 Coarse-Grained Force Field: Small Molecules
Martini 3 Coarse-Grained Force Field: Small Molecules Open
The recent re-parametrization of the Martini coarse-grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. Here, we describe how small molecule…
View article: Martini 3 Coarse-Grained Force Field: Small Molecules
Martini 3 Coarse-Grained Force Field: Small Molecules Open
The recent re-parametrization of the Martini coarse-grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. Here, we describe how small molecule…
View article: Martini 3: a general purpose force field for coarse-grained molecular dynamics
Martini 3: a general purpose force field for coarse-grained molecular dynamics Open