Machine learning force fields

OT Unke, S Chmiela, HE Sauceda… - Chemical …, 2021 - ACS Publications
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 …

Using metadynamics to explore complex free-energy landscapes

G Bussi, A Laio - Nature Reviews Physics, 2020 - nature.com
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 …

Automated exploration of the low-energy chemical space with fast quantum chemical methods

P Pracht, F Bohle, S Grimme - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
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 …

[HTML][HTML] DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

B Hourahine, B Aradi, V Blum, F Bonafe… - The Journal of …, 2020 - pubs.aip.org
DFTB+ is a versatile community developed open source software package offering fast and
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 …

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 …

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 …

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 …

Improving the accuracy of atomistic simulations of the electrochemical interface

R Sundararaman, D Vigil-Fowler, K Schwarz - Chemical reviews, 2022 - ACS Publications
Atomistic simulation of the electrochemical double layer is an ambitious undertaking,
requiring quantum mechanical description of electrons, phase space sampling of liquid …

Broadly neutralizing antibodies target a haemagglutinin anchor epitope

JJ Guthmiller, J Han, HA Utset, L Li, LYL Lan, C Henry… - Nature, 2022 - nature.com
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus
have the potential to provide near universal protection against influenza virus infection …