Loop dynamics and the evolution of enzyme activity

M Corbella, GP Pinto, SCL Kamerlin - Nature Reviews Chemistry, 2023 - nature.com
In the early 2000s, Tawfik presented his 'New View'on enzyme evolution, highlighting the
role of conformational plasticity in expanding the functional diversity of limited repertoires of …

Navigating the landscape of enzyme design: from molecular simulations to machine learning

J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …

Reactzyme: A benchmark for enzyme-reaction prediction

C Hua, B Zhong, S Luan, L Hong… - Advances in …, 2025 - proceedings.neurips.cc
Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life,
enabling diverse biological processes and adaptations. Predicting enzyme functions is …

Perspectives on computational enzyme modeling: from mechanisms to design and drug development

K Nam, Y Shao, DT Major, M Wolf-Watz - ACS omega, 2024 - ACS Publications
Understanding enzyme mechanisms is essential for unraveling the complex molecular
machinery of life. In this review, we survey the field of computational enzymology …

Enabling high-throughput enzyme discovery and engineering with a low-cost, robot-assisted pipeline

B Norton-Baker, MCR Denton, NP Murphy, B Fram… - Scientific Reports, 2024 - nature.com
As genomic databases expand and artificial intelligence tools advance, there is a growing
demand for efficient characterization of large numbers of proteins. To this end, here we …

Ancestral Sequence Reconstruction for Designing Biocatalysts and Investigating their Functional Mechanisms

K Prakinee, S Phaisan, S Kongjaroon, P Chaiyen - JACS Au, 2024 - ACS Publications
Biocatalysis has emerged as a green approach for efficient and sustainable production in
various industries. In recent decades, numerous advancements in computational and …

Modern computational methods for rational enzyme engineering

P Ferreira, PA Fernandes, MJ Ramos - Chem Catalysis, 2022 - cell.com
Biocatalysis is a thriving field of research because of the vast, environmentally friendly
impact that enzymes have on industry and biotechnology. However, in most production …

Enzymeflow: Generating reaction-specific enzyme catalytic pockets through flow matching and co-evolutionary dynamics

C Hua, Y Liu, D Zhang, O Zhang, S Luan… - arxiv preprint arxiv …, 2024 - arxiv.org
Enzyme design is a critical area in biotechnology, with applications ranging from drug
development to synthetic biology. Traditional methods for enzyme function prediction or …

[HTML][HTML] Archaeal lipolytic enzymes: current developments and further prospects

GK Meghwanshi, S Verma, V Srivastava… - Biotechnology Advances, 2022 - Elsevier
Lipolytic enzymes include triacylglycerol lipases (EC 3.1. 1.3) and esterases (EC 3.1. 1.1)
that catalyze the cleavage and formation of ester bonds. They are potential industrial …

Efficient exploration of sequence space by sequence-guided protein engineering and design

BE Clifton, D Kozome, P Laurino - Biochemistry, 2022 - ACS Publications
The rapid growth of sequence databases over the past two decades means that protein
engineers faced with optimizing a protein for any given task will often have immediate …