Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

[HTML][HTML] Predictive chemistry: machine learning for reaction deployment, reaction development, and reaction discovery

Z Tu, T Stuyver, CW Coley - Chemical science, 2023 - pubs.rsc.org
The field of predictive chemistry relates to the development of models able to describe how
molecules interact and react. It encompasses the long-standing task of computer-aided …

[HTML][HTML] Can electric fields drive chemistry for an aqueous microdroplet?

H Hao, I Leven, T Head-Gordon - Nature communications, 2022 - nature.com
Reaction rates of common organic reactions have been reported to increase by one to six
orders of magnitude in aqueous microdroplets compared to bulk solution, but the reasons for …

Electric-field mediated chemistry: uncovering and exploiting the potential of (oriented) electric fields to exert chemical catalysis and reaction control

S Shaik, D Danovich, J Joy, Z Wang… - Journal of the American …, 2020 - ACS Publications
This Perspective discusses oriented external-electric-fields (OEEF), and other electric-field
types, as “smart reagents”, which enable in principle control over wide-ranging aspects of …

Enzymatic noncovalent synthesis

H He, W Tan, J Guo, M Yi, AN Shy, B Xu - Chemical reviews, 2020 - ACS Publications
Enzymatic reactions and noncovalent (ie, supramolecular) interactions are two fundamental
nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process …

[HTML][HTML] Data-informed discovery of hydrolytic nanozymes

S Li, Z Zhou, Z Tie, B Wang, M Ye, L Du, R Cui… - Nature …, 2022 - nature.com
Nanozyme is a collection of nanomaterials with enzyme-like activity but higher
environmental tolerance and long-term stability than their natural counterparts. Improving …

Large-scale production of enzymes for biotechnology uses

A Fasim, VS More, SS More - Current opinion in biotechnology, 2021 - Elsevier
Enzymes are biocatalysts that speed up the chemical reaction to obtain the final valuable
product/s. Biotechnology has revolutionized the use of traditional enzymes to be applicable …

Automated in silico design of homogeneous catalysts

M Foscato, VR Jensen - ACS catalysis, 2020 - ACS Publications
Catalyst discovery is increasingly relying on computational chemistry, and many of the
computational tools are currently being automated. The state of this automation and the …

Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory

E Kraka, W Zou, Y Tao - Wiley Interdisciplinary Reviews …, 2020 - Wiley Online Library
Modern vibrational spectroscopy is more than just an analytical tool. Information about the
electronic structure of a molecule, the strength of its bonds, and its conformational flexibility …

A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site

C Zheng, Y Mao, J Kozuch, AO Atsango, Z Ji… - Nature …, 2022 - nature.com
The catalytic power of an electric field depends on its magnitude and orientation with respect
to the reactive chemical species. Understanding and designing new catalysts for …