Concept
Comparison of software for molecular mechanics modeling
Related publications (33)
Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach
Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...
Swiss Chemical Soc2024Efficient and insightful descriptors for representing molecular and material space
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 ...
EPFL2024Applications of the thawed Gaussian approximation to electronic spectroscopy.
The exploration of electronically excited states and the study of diverse photochemical and photophysical processes are the main goals of molecular electronic spectroscopy. Exact quantum-mechanical simulation of such experiments is, however, beyond current ...
EPFL2024Atomic-level structure determination of amorphous molecular solids by NMR
David Lyndon Emsley, Arthur César Pinon, Pinelopi Moutzouri, Manuel Cordova
Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder ...
Berlin2023Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers
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 ...
2020ONETEP plus TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory
We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlate ...
2020Bimolecular charge transfer reactions at and through the liquid-liquid interface
Interfaces are ubiquitous in Nature. Among them, soft interfaces are essential constituents of biological tissues. Indeed, many electrochemical reactions and phenomena take place at these interfaces. In this respect, ITIES are an interesting model to study ...
EPFL2019Coupled Atomistics and Discrete Dislocations in 3d (CADD-3d)
Jean-François Molinari, William Curtin, Guillaume Anciaux, Till Junge, Jaehyun Cho, Max Ludwig Hodapp
Capturing plasticity at realistic dislocation densities with high configurational complexity requires a continuum-leveldiscrete dislocation dynamics (DDD) description. However, many features controlling dislocation motion areinherently atomistic, such as t ...
2018Coupled Atomistics and Discrete Dislocations in 3d (CADD-3d)
Capturing plasticity at realistic dislocation densities with high configurational complexity requires a continuum-level discrete dislocation dynamics (DDD) description. However, many features controlling dislocation motion are inherently atomistic, such as ...
2018Using PyMOL as a platform for computational drug design
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