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 …

Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) approach

JS Grassano, I Pickering, AE Roitberg… - Journal of Chemical …, 2024 - ACS Publications
Machine learning (ML) methods have reached high accuracy levels for the prediction of in
vacuo molecular properties. However, the simulation of large systems solely through ML …

[HTML][HTML] Acidity and nucleophilic reactivity of glutathione persulfide

D Benchoam, JA Semelak, E Cuevasanta… - Journal of Biological …, 2020 - Elsevier
Persulfides (RSSH/RSS−) participate in sulfur trafficking and metabolic processes, and are
proposed to mediate the signaling effects of hydrogen sulfide (H 2 S). Despite their growing …

[HTML][HTML] Recent advances in QM/MM free energy calculations using reference potentials

F Duarte, BA Amrein, D Blaha-Nelson… - Biochimica et Biophysica …, 2015 - Elsevier
Background Recent years have seen enormous progress in the development of methods for
modeling (bio) molecular systems. This has allowed for the simulation of ever larger and …

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

GD Mirón, JA Semelak, L Grisanti, A Rodriguez… - Nature …, 2023 - nature.com
Challenging the basis of our chemical intuition, recent experimental evidence reveals the
presence of a new type of intrinsic fluorescence in biomolecules that exists even in the …

Highly efficient resolution-of-identity density functional theory calculations on central and graphics processing units

J Kussmann, H Laqua… - Journal of Chemical Theory …, 2021 - ACS Publications
We present an efficient method to evaluate Coulomb potential matrices using the resolution
of identity approximation and semilocal exchange-correlation potentials on central (CPU) …

Nanoscale multireference quantum chemistry: Full configuration interaction on graphical processing units

BS Fales, BG Levine - Journal of Chemical Theory and …, 2015 - ACS Publications
Methods based on a full configuration interaction (FCI) expansion in an active space of
orbitals are widely used for modeling chemical phenomena such as bond breaking, multiply …

Dynamical properties of enzyme–substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density …

MG Khrenova, VG Tsirelson… - Physical Chemistry …, 2020 - pubs.rsc.org
A dynamical approach is proposed to discriminate between reactive (rES) and nonreactive
(nES) enzyme–substrate complexes taking the SARS-CoV-2 main protease (Mpro) as an …

Parallel implementation of density functional theory methods in the quantum interaction computational kernel program

M Manathunga, Y Miao, D Mu, AW Götz… - Journal of Chemical …, 2020 - ACS Publications
We present the details of a graphics processing unit (GPU) capable exchange correlation
(XC) scheme integrated into the open source QUantum Interaction Computational Kernel …

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

AD Stephens, MN Qaisrani, MT Ruggiero… - Proceedings of the …, 2021 - pnas.org
Fluorescence in biological systems is usually associated with the presence of aromatic
groups. Here, by employing a combined experimental and computational approach, we …