Deep learning for computational chemistry

GB Goh, NO Hodas, A Vishnu - Journal of computational …, 2017 - Wiley Online Library
The rise and fall of artificial neural networks is well documented in the scientific literature of
both computer science and computational chemistry. Yet almost two decades later, we are …

Carbon nanodots from an in silico perspective

F Mocci, L de Villiers Engelbrecht, C Olla… - Chemical …, 2022 - ACS Publications
Carbon nanodots (CNDs) are the latest and most shining rising stars among
photoluminescent (PL) nanomaterials. These carbon-based surface-passivated …

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

J Huang, S Rauscher, G Nawrocki, T Ran, M Feig… - Nature …, 2017 - nature.com
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling
and simulations. We present its refinement, CHARMM36m (http://mackerell. umaryland …

Beyond shielding: the roles of glycans in the SARS-CoV-2 spike protein

L Casalino, Z Gaieb, JA Goldsmith, CK Hjorth… - ACS central …, 2020 - ACS Publications
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 …

Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors

SA Moghadasi, E Heilmann, AM Khalil, C Nnabuife… - Science …, 2023 - science.org
Vaccines and drugs have helped reduce disease severity and blunt the spread of severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ongoing virus …

Accelerating the prediction and discovery of peptide hydrogels with human-in-the-loop

T Xu, J Wang, S Zhao, D Chen, H Zhang… - Nature …, 2023 - nature.com
The amino acid sequences of peptides determine their self-assembling properties. Accurate
prediction of peptidic hydrogel formation, however, remains a challenging task. This work …

[HTML][HTML] SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma

E Andreano, G Piccini, D Licastro, L Casalino… - BioRxiv, 2020 - ncbi.nlm.nih.gov
To investigate the evolution of SARS-CoV-2 in the immune population, we co-incubated
authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The …

[HTML][HTML] Less is more: Sampling chemical space with active learning

JS Smith, B Nebgen, N Lubbers, O Isayev… - The Journal of …, 2018 - pubs.aip.org
The development of accurate and transferable machine learning (ML) potentials for
predicting molecular energetics is a challenging task. The process of data generation to train …

Structure of the µ-opioid receptor–Gi protein complex

A Koehl, H Hu, S Maeda, Y Zhang, Q Qu, JM Paggi… - Nature, 2018 - nature.com
The μ-opioid receptor (μOR) is a G-protein-coupled receptor (GPCR) and the target of most
clinically and recreationally used opioids. The induced positive effects of analgesia and …

High-resolution structure and strain comparison of infectious mammalian prions

A Kraus, F Hoyt, CL Schwartz, B Hansen, E Artikis… - Molecular cell, 2021 - cell.com
Within the extensive range of self-propagating pathologic protein aggregates of mammals,
prions are the most clearly infectious (eg,∼ 10 9 lethal doses per milligram). The structures …