Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction

CR Baiz, B Błasiak, J Bredenbeck, M Cho… - Chemical …, 2020 - ACS Publications
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and
studies of functional materials. Over the past decade, various coherent nonlinear vibrational …

Molecular dynamics simulation for all

SA Hollingsworth, RO Dror - Neuron, 2018 - cell.com
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

AmberTools

DA Case, HM Aktulga, K Belfon… - Journal of chemical …, 2023 - ACS Publications
AmberTools | Journal of Chemical Information and Modeling ACS ACS Publications C&EN CAS
Find my institution Log In Journal of Chemical Information and Modeling ACS Publications …

gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS

MS Valdés-Tresanco… - Journal of chemical …, 2021 - ACS Publications
Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …

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 …

Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution

TN Starr, AJ Greaney, WW Hannon, AN Loes, K Hauser… - Science, 2022 - science.org
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved variants with
substitutions in the spike receptor-binding domain (RBD) that affect its affinity for angiotensin …

Two-photon nanoprobes based on bioorganic nanoarchitectonics with a photo-oxidation enhanced emission mechanism

S Li, R Chang, L Zhao, R **ng, JCM van Hest… - Nature …, 2023 - nature.com
Two-photon absorption (TPA) fluorescence imaging holds great promise in diagnostics and
biomedicine owing to its unparalleled spatiotemporal resolution. However, the adaptability …

Insights into distinct signaling profiles of the µOR activated by diverse agonists

Q Qu, W Huang, D Aydin, JM Paggi, AB Seven… - Nature chemical …, 2023 - nature.com
Drugs targeting the μ-opioid receptor (μOR) are the most effective analgesics available but
are also associated with fatal respiratory depression through a pathway that remains …

Direct visible-light-excited flavoproteins for redox-neutral asymmetric radical hydroarylation

B Zhao, J Feng, L Yu, Z **ng, B Chen, A Liu, F Liu… - Nature Catalysis, 2023 - nature.com
State-of-the-art non-natural photoenzymatic catalysis typically relies on either ultraviolet light
activation or the formation of electron donor–acceptor complexes. Inspired by nature, herein …

ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution

C Tian, K Kasavajhala, KAA Belfon… - Journal of chemical …, 2019 - ACS Publications
Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …