Tools for computational design and high-throughput screening of therapeutic enzymes

M Vasina, J Velecký, J Planas-Iglesias… - Advanced Drug Delivery …, 2022 - Elsevier
Therapeutic enzymes are valuable biopharmaceuticals in various biomedical applications.
They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement …

Web-based tools for computational enzyme design

SM Marques, J Planas-Iglesias, J Damborsky - Current Opinion in Structural …, 2021 - Elsevier
Highlights•Enzymes are increasingly used in technological applications but often require
prior optimization.•Computational tools save time and effort in protein engineering …

FLIP: Benchmark tasks in fitness landscape inference for proteins

C Dallago, J Mou, KE Johnston, BJ Wittmann… - bioRxiv, 2021 - biorxiv.org
Abstract Machine learning could enable an unprecedented level of control in protein
engineering for therapeutic and industrial applications. Critical to its use in designing …

FireProtDB: database of manually curated protein stability data

J Stourac, J Dubrava, M Musil, J Horackova… - Nucleic acids …, 2021 - academic.oup.com
The majority of naturally occurring proteins have evolved to function under mild conditions
inside the living organisms. One of the critical obstacles for the use of proteins in …

Computer-aided understanding and engineering of enzymatic selectivity

L Wu, L Qin, Y Nie, Y Xu, YL Zhao - Biotechnology Advances, 2022 - Elsevier
Abstract Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric
synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally …

Updates on drug designing approach through computational strategies: a review

I Azad, T Khan, N Ahmad, AR Khan, Y Akhter - Future Science OA, 2023 - Taylor & Francis
The drug discovery and development (DDD) process in pursuit of novel drug candidates is a
challenging procedure requiring lots of time and resources. Therefore, computer-aided drug …

[HTML][HTML] Enhancing the Catalytic Activity of Type II L-Asparaginase from Bacillus licheniformis through Semi-Rational Design

Y Zhou, L Jiao, J Shen, H Chi, Z Lu, H Liu, F Lu… - International Journal of …, 2022 - mdpi.com
Low catalytic activity is a key factor limiting the widespread application of type II L-
asparaginase (ASNase) in the food and pharmaceutical industries. In this study, smart …

[HTML][HTML] Prospects of using biocatalysis for the synthesis and modification of polymers

M Nikulin, V Švedas - Molecules, 2021 - mdpi.com
Trends in the dynamically developing application of biocatalysis for the synthesis and
modification of polymers over the past 5 years are considered, with an emphasis on the …

Substrate Anchoring and Flexibility Reduction in CYP153AM.aq Leads to Highly Improved Efficiency toward Octanoic Acid

LR Rapp, SM Marques, E Zukic, B Rowlinson… - ACS …, 2021 - ACS Publications
Cytochrome P450 CYP153A M. aq from Marinobacter aquaeolei serves as a model enzyme
for the terminal (ω-) hydroxylation of medium-to long-chain fatty acids. We have engineered …

[HTML][HTML] 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 …