Directed evolution: methodologies and applications

Y Wang, P Xue, M Cao, T Yu, ST Lane… - Chemical reviews, 2021 - ACS Publications
Directed evolution aims to expedite the natural evolution process of biological molecules
and systems in a test tube through iterative rounds of gene diversifications and library …

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 …

[HTML][HTML] PremPS: Predicting the impact of missense mutations on protein stability

Y Chen, H Lu, N Zhang, Z Zhu, S Wang… - PLoS computational …, 2020 - journals.plos.org
Computational methods that predict protein stability changes induced by missense
mutations have made a lot of progress over the past decades. Most of the available methods …

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

R Nikam, A Kulandaisamy, K Harini… - Nucleic acids …, 2021 - academic.oup.com
ProThermDB is an updated version of the thermodynamic database for proteins and mutants
(ProTherm), which has∼ 31 500 data on protein stability, an increase of 84% from the …

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

DEV Pires, DB Ascher, TL Blundell - Nucleic acids research, 2014 - academic.oup.com
Cancer genome and other sequencing initiatives are generating extensive data on non-
synonymous single nucleotide polymorphisms (nsSNPs) in human and other genomes. In …

Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure

M Rahban, S Zolghadri, N Salehi, F Ahmad… - International journal of …, 2022 - Elsevier
Increasing the temperature by just a few degrees may lead to structural perturbation or
unfolding of the protein and consequent loss of function. The concepts of flexibility and …

[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 …

DeepDDG: predicting the stability change of protein point mutations using neural networks

H Cao, J Wang, L He, Y Qi… - Journal of chemical …, 2019 - ACS Publications
Accurately predicting changes in protein stability due to mutations is important for protein
engineering and for understanding the functional consequences of missense mutations in …

Refactored genetic codes enable bidirectional genetic isolation

JF Zürcher, WE Robertson, T Kappes, G Petris… - Science, 2022 - science.org
The near-universal genetic code defines the correspondence between codons in genes and
amino acids in proteins. We refactored the structure of the genetic code in Escherichia coli …

Stability effects of mutations and protein evolvability

N Tokuriki, DS Tawfik - Current opinion in structural biology, 2009 - Elsevier
The past several years have seen novel insights at the interface of protein biophysics and
evolution. The accepted paradigm that proteins can tolerate nearly any amino acid …