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 …

Biomolecular modeling thrives in the age of technology

T Schlick, S Portillo-Ledesma - Nature computational science, 2021 - nature.com
The biomolecular modeling field has flourished since its early days in the 1970s due to the
rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase …

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

TN Starr, N Czudnochowski, Z Liu, F Zatta, YJ Park… - Nature, 2021 - nature.com
An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape,–, have activity
against diverse sarbecoviruses,,–, and be highly protective through viral neutralization,,–and …

[HTML][HTML] The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

J Cubuk, JJ Alston, JJ Incicco, S Singh… - Nature …, 2021 - nature.com
Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein
critical for viral genome packaging, yet the molecular details that underlie this process are …

[HTML][HTML] Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

EC Thomson, LE Rosen, JG Shepherd, R Spreafico… - Cell, 2021 - cell.com
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging
vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS …

A multiscale coarse-grained model of the SARS-CoV-2 virion

A Yu, AJ Pak, P He, V Monje-Galvan, L Casalino… - Biophysical journal, 2021 - cell.com
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent
of the COVID-19 pandemic. Computer simulations of complete viral particles can provide …

Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: modeling and simulation approaches

A Frances-Monerris, C Hognon, T Miclot… - Journal of Proteome …, 2020 - ACS Publications
The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the
breakthrough of the COVID-19 pandemic that is presently affecting a growing number of …

Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 main protease

T Sztain, R Amaro, JA McCammon - Journal of chemical …, 2021 - ACS Publications
The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health
concern. Many quests to computationally identify treatments against the virus rely on in silico …

Accurate machine learned quantum-mechanical force fields for biomolecular simulations

OT Unke, M Stöhr, S Ganscha, T Unterthiner… - arXiv preprint arXiv …, 2022 - arxiv.org
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological
processes. Accurate MD simulations require computationally demanding quantum …

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

TJ Inizan, F Célerse, O Adjoua, D El Ahdab… - Chemical …, 2021 - pubs.rsc.org
We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale
molecular dynamics (MD) simulations of large biosystems using many-body polarizable …