Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

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 …

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 …

AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings

J Eberhardt, D Santos-Martins… - Journal of chemical …, 2021 - ACS Publications
AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

Structures of the σ2 receptor enable docking for bioactive ligand discovery

A Alon, J Lyu, JM Braz, TA Tummino, V Craik… - Nature, 2021 - nature.com
The σ2 receptor has attracted intense interest in cancer imaging, psychiatric disease,
neuropathic pain,–and other areas of biology,. Here we determined the crystal structure of …

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 …

[HTML][HTML] Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Q Mao, M Feng, XZ Jiang, Y Ren, KH Luo… - Progress in Energy and …, 2023 - Elsevier
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …

Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor

EA Fink, J Xu, H Hübner, JM Braz, P Seemann, C Avet… - Science, 2022 - science.org
Because nonopioid analgesics are much sought after, we computationally docked more
than 301 million virtual molecules against a validated pain target, the α2A-adrenergic …

[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]

AT Bogetti, B Mostofian, A Dickson… - Living journal of …, 2019 - ncbi.nlm.nih.gov
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Tinker 8: software tools for molecular design

JA Rackers, Z Wang, C Lu, ML Laury… - Journal of chemical …, 2018 - ACS Publications
The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …