Machine learning force fields
In recent years, the use of machine learning (ML) in computational chemistry has enabled
numerous advances previously out of reach due to the computational complexity of …
numerous advances previously out of reach due to the computational complexity of …
Using metadynamics to explore complex free-energy landscapes
Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …
acceleration of rare events and estimation of the free energy of complex molecular systems …
Automated exploration of the low-energy chemical space with fast quantum chemical methods
We propose and discuss an efficient scheme for the in silico sampling for parts of the
molecular chemical space by semiempirical tight-binding methods combined with a meta …
molecular chemical space by semiempirical tight-binding methods combined with a meta …
[HTML][HTML] DFTB+, a software package for efficient approximate density functional theory based atomistic simulations
DFTB+ is a versatile community developed open source software package offering fast and
efficient methods for carrying out atomistic quantum mechanical simulations. By …
efficient methods for carrying out atomistic quantum mechanical simulations. By …
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods, 2019 - nature.com
The PLUMED consortium unifies developers and contributors to PLUMED, an open-source
library for enhanced-sampling, free-energy calculations and the analysis of molecular …
library for enhanced-sampling, free-energy calculations and the analysis of molecular …
Exploration of chemical compound, conformer, and reaction space with meta-dynamics simulations based on tight-binding quantum chemical calculations
S Grimme - Journal of chemical theory and computation, 2019 - ACS Publications
The semiempirical tight-binding based quantum chemistry method GFN2-xTB is used in the
framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and …
framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and …
Deep learning the slow modes for rare events sampling
L Bonati, GM Piccini… - Proceedings of the …, 2021 - National Acad Sciences
The development of enhanced sampling methods has greatly extended the scope of
atomistic simulations, allowing long-time phenomena to be studied with accessible …
atomistic simulations, allowing long-time phenomena to be studied with accessible …
Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview
V Salmaso, S Moro - Frontiers in pharmacology, 2018 - frontiersin.org
Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …
1980s. Given the low computational resources of the time, the first molecular modeling …
Improving the accuracy of atomistic simulations of the electrochemical interface
Atomistic simulation of the electrochemical double layer is an ambitious undertaking,
requiring quantum mechanical description of electrons, phase space sampling of liquid …
requiring quantum mechanical description of electrons, phase space sampling of liquid …
Broadly neutralizing antibodies target a haemagglutinin anchor epitope
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus
have the potential to provide near universal protection against influenza virus infection …
have the potential to provide near universal protection against influenza virus infection …