Publications related to Molecular graphics

Machine learning-aided generative molecular design

Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...

Nature Portfolio2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

2023 Roadmap on molecular modelling of electrochemical energy materials

Alfredo Pasquarello, Chunmin Zhang, Assil Bouzid

New materials for electrochemical energy storage and conversion are the key to the electrification and sustainable development of our modern societies. Molecular modelling based on the principles of quantum mechanics and statistical mechanics as well as em ...

Iop Publishing Ltd2023

Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits

Matteo Dal Peraro, Luciano Andres Abriata, Fabio Jose Cortes Rodriguez, Lucien Fabrice Krapp

moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. ...

SWISS CHEMICAL SOC2022

Random conical tilt reconstruction without particle picking in cryo-electron microscopy

Nicolas Boumal

A method is proposed to reconstruct the 3D molecular structure from micrographs collected at just one sample tilt angle in the random conical tilt scheme in cryo-electron microscopy. The method uses autocorrelation analysis on the micrographs to estimate f ...

INT UNION CRYSTALLOGRAPHY2022

Investigation of the specificity and mechanism of action of the ULK1/AMPK inhibitor SBI-0206965

Kei Sakamoto, Katyayanee Neopane

SBI-0206965, originally identified as an inhibitor of the autophagy initiator kinase ULK1, has recently been reported as a more potent and selective AMP-activated protein kinase (AMPK) inhibitor relative to the widely used, but promiscuous inhibitor Compou ...

2021

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

Daniel Constam, Benjamin Marcel Daniel Rothé

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examin ...

Nature Portfolio2021

Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials

Luc Sébastien Bondaz, Rohit Karnik

Nanoporous single-layer graphene is promising as an ideal membrane because of its extreme thinness, chemical resistance, and mechanical strength, provided that selective nanopores are successfully incorporated. However, screening and understanding the tran ...

AIP Publishing2021

Trametinib Induces the Stabilization of a Dual GNAQ p.Gly48Leu-and FGFR4 p.Cys172Gly-Mutated Uveal Melanoma. The Role of Molecular Modelling in Personalized Oncology

Olivier Michielin, Krisztian Homicsko, Alexandre Wicky

We report a case of an uveal melanoma patient with GNAQ p.Gly48Leu who responded to MEK inhibition. At the time of the molecular analysis, the pathogenicity of the mutation was unknown. A tridimensional structural analysis showed that G alpha(q) can adopt ...

2020

Delivery of a Masked Uranium(II) by an Oxide-Bridged Diuranium(III) Complex

Marinella Mazzanti, Farzaneh Fadaei Tirani, Dieuwertje Katelijn Modder

Oxide is an attractive linker for building polymetallic complexes that provide molecular models for metal oxide activity, but studies of these systems are limited to metals in high oxidation states. Herein, we synthesized and characterized the molecular an ...

Wiley-VCH Verlag GmbH2021

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano Andres Abriata

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, m ...

2020

Spectro-electrochemical toolbox for monitoring and controlling quinone-mediated redox-driven molecular gripping

Jovana Milic, Thomas Schneeberger

The control of molecular systems by electrical charge or light is a prerequisite for their application in nanoelectronics. Such potential has been uniquely exploited in quinone-based resorcin[4]arene cavitands that can act as molecular grippers, reversibly ...

2019

The Quest for Molecular Grippers: Photo-Electric Control of Molecular Gripping Machinery

Jovana Milic

The quest for nanoscale molecular machines has inspired the search for their close relatives, molecular grippers. This path was paved by the development of resorcin[4]arene cavitands and their quinone-based redox-active congeners. In this Concept article, ...

2019

Accurate molecular polarizabilities with coupled cluster theory and machine learning

Michele Ceriotti, David Mark Wilkins, Andrea Grisafi, Yang Yang

The molecular dipole polarizability describes the tendency of a molecule to change its dipole moment in response to an applied electric field. This quantity governs key intra- and intermolecular interactions, such as induction and dispersion; plays a vital ...

2019

Modeling robot geometries like molecules, application to fast multi-contact posture planning for humanoids

Auke Ijspeert, Salman Faraji

Traditional joint-space models used to describe equations of motion for humanoid robots offer nice properties linked directly to the way these robots are built. However, from a computational point of view and convergence properties, these models are not th ...

Ieee-Inst Electrical Electronics Engineers Inc2018

Using PyMOL as a platform for computational drug design

Shuguang Yuan, Zhenquan Hu

PyMOL, a cross-platform molecular graphics tool, has been widely used for three-dimensional (3D) visualization of proteins, nucleic acids, small molecules, electron densities, surfaces, and trajectories. It is also capable of editing molecules, ray tracing ...

Wiley2017

Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties

Ursula Röthlisberger, Anatole von Lilienfeld, Nicholas John Browning

The training of molecular models of quantum mechanical properties based on statistical machine learning requires large data sets which exemplify the map from chemical structure to molecular property. Intelligent a priori selection of training examples is o ...

2017

Photoinduced Structural Dynamics of Molecular Systems Mapped by Time-Resolved X-ray Methods

Majed Chergui

We review the tremendous advances in ultrafast X-ray science, over the past 15 years, making the best use of new ultrashort X-ray sources including table-top or large-scale facilities. Different complementary X-ray-based techniques, including spectroscopy, ...

American Chemical Society2017

Studying membrane-protein interplay by modeling realistic conditions

Martina Audagnotto

Realistic models of cellular environments have long captured the imagination of biologists and physical scientists. More than 20 years ago, Goodshellâ s inspiring rendering of cellular environments provided the foundation for the idea of capturing the ful ...

EPFL2017

What interactions can distort the orientational distribution of interfacial water molecules as probed by second harmonic and sum frequency generation?

Sylvie Roke

Aqueous interfaces are omnipresent in nature. Nonlinear optical methods such as second harmonic and sum frequency generation (SHG/SFG) are valuable techniques to access molecular level information from these interfaces. In the interpretation of SHG and SFG ...

American Institute of Physics2016