Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D **, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …

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 …

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 …

A general temperature-guided language model to design proteins of enhanced stability and activity

F Jiang, M Li, J Dong, Y Yu, X Sun, B Wu, J Huang… - Science …, 2024 - science.org
Designing protein mutants with both high stability and activity is a critical yet challenging
task in protein engineering. Here, we introduce PRIME, a deep learning model, which can …

ProSTAGE: predicting effects of mutations on protein stability by using protein embeddings and graph convolutional networks

G Li, S Yao, L Fan - Journal of Chemical Information and …, 2024 - ACS Publications
Protein thermodynamic stability is essential to clarify the relationships among structure,
function, and interaction. Therefore, develo** a faster and more accurate method to …

[HTML][HTML] DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences

M Li, H Wang, Z Yang, L Zhang, Y Zhu - Computational and Structural …, 2023 - Elsevier
Thermally stable proteins find extensive applications in industrial production,
pharmaceutical development, and serve as a highly evolved starting point in protein …

[HTML][HTML] Protein structure-based evaluation of missense variants: Resources, challenges and future directions

A David, MJE Sternberg - Current Opinion in Structural Biology, 2023 - Elsevier
We provide an overview of the methods that can be used for protein structure-based
evaluation of missense variants. The algorithms can be broadly divided into those that …

[HTML][HTML] Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications

J Sun, A Kulandaisamy, J Liu, K Hu… - Computational and …, 2023 - Elsevier
Membrane proteins mediate a wide spectrum of biological processes, such as signal
transduction and cell communication. Due to the arduous and costly nature inherent to the …

[HTML][HTML] SoluProtMutDB: A manually curated database of protein solubility changes upon mutations

J Velecký, M Hamsikova, J Stourac, M Musil… - Computational and …, 2022 - Elsevier
Protein solubility is an attractive engineering target primarily due to its relation to yields in
protein production and manufacturing. Moreover, better knowledge of the mutational effects …

MPTherm-pred: analysis and prediction of thermal stability changes upon mutations in transmembrane proteins

A Kulandaisamy, J Zaucha, D Frishman… - Journal of Molecular …, 2021 - Elsevier
The stability of membrane proteins differs from globular proteins due to the presence of
nonpolar membrane-spanning regions. Using a dataset of 929 membrane protein mutations …