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Protein design: From the aspect of water solubility and stability
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 …
sequence and 3D-conformation. Their manipulation represents important aspects of the …
Tools for computational design and high-throughput screening of therapeutic enzymes
Therapeutic enzymes are valuable biopharmaceuticals in various biomedical applications.
They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement …
They have been successfully applied for fibrinolysis, cancer treatment, enzyme replacement …
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years
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 …
(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 …
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 …
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 …
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 …
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
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 …
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
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 …
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
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 …
nonpolar membrane-spanning regions. Using a dataset of 929 membrane protein mutations …