Opportunities and challenges in design and optimization of protein function

D Listov, CA Goverde, BE Correia… - … Reviews Molecular Cell …, 2024 - nature.com
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …

Advances in protein structure prediction and design

B Kuhlman, P Bradley - Nature reviews molecular cell biology, 2019 - nature.com
The prediction of protein three-dimensional structure from amino acid sequence has been a
grand challenge problem in computational biophysics for decades, owing to its intrinsic …

Computational redesign of a PETase for plastic biodegradation under ambient condition by the GRAPE strategy

Y Cui, Y Chen, X Liu, S Dong, Y Tian, Y Qiao… - Acs …, 2021 - ACS Publications
Nature has provided a fantastic array of enzymes that are responsible for essential
biochemical functions but not usually suitable for technological applications. Not content …

Transfer learning to leverage larger datasets for improved prediction of protein stability changes

H Dieckhaus, M Brocidiacono, NZ Randolph… - Proceedings of the …, 2024 - pnas.org
Amino acid mutations that lower a protein's thermodynamic stability are implicated in
numerous diseases, and engineered proteins with enhanced stability can be important in …

Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability

Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

Building enzymes through design and evolution

EJ Hossack, FJ Hardy, AP Green - ACS Catalysis, 2023 - ACS Publications
Designing efficient enzymes is a formidable challenge at the forefront of modern
biocatalysis. Here, we review recent developments in the field and illustrate how the …

FireProt 2.0: web-based platform for the fully automated design of thermostable proteins

M Musil, A Jezik, J Horackova, S Borko… - Briefings in …, 2024 - academic.oup.com
Thermostable proteins find their use in numerous biomedical and biotechnological
applications. However, the computational design of stable proteins often results in single …

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

L Sumbalova, J Stourac, T Martinek… - Nucleic acids …, 2018 - academic.oup.com
HotSpot Wizard is a web server used for the automated identification of hotspots in semi-
rational protein design to give improved protein stability, catalytic activity, substrate …

Recent advances in the improvement of enzyme thermostability by structure modification

Z Xu, YK Cen, SP Zou, YP Xue… - Critical reviews in …, 2020 - Taylor & Francis
Thermostability is considered to be an important parameter to measure the feasibility of
enzymes for industrial applications. Generally, higher thermostability makes an enzyme …

[HTML][HTML] FoldX as protein engineering tool: better than random based approaches?

O Buß, J Rudat, K Ochsenreither - Computational and structural …, 2018 - Elsevier
Improving protein stability is an important goal for basic research as well as for clinical and
industrial applications but no commonly accepted and widely used strategy for efficient …