Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Machine learning in enzyme engineering

S Mazurenko, Z Prokop, J Damborsky - ACS Catalysis, 2019 - ACS Publications
Enzyme engineering plays a central role in developing efficient biocatalysts for
biotechnology, biomedicine, and life sciences. Apart from classical rational design and …

SoluProt: prediction of soluble protein expression in Escherichia coli

J Hon, M Marusiak, T Martinek, A Kunka… - …, 2021 - academic.oup.com
Motivation Poor protein solubility hinders the production of many therapeutic and industrially
useful proteins. Experimental efforts to increase solubility are plagued by low success rates …

Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE

C Wang, Q Zou - BMC biology, 2023 - Springer
Background Protein solubility is a precondition for efficient heterologous protein expression
at the basis of most industrial applications and for functional interpretation in basic research …

Computational design of stable and soluble biocatalysts

M Musil, H Konegger, J Hon, D Bednar… - Acs Catalysis, 2018 - ACS Publications
Natural enzymes are delicate biomolecules possessing only marginal thermodynamic
stability. Poorly stable, misfolded, and aggregated proteins lead to huge economic losses in …

DSResSol: A sequence-based solubility predictor created with Dilated Squeeze Excitation Residual Networks

M Madani, K Lin, A Tarakanova - International Journal of Molecular …, 2021 - mdpi.com
Protein solubility is an important thermodynamic parameter that is critical for the
characterization of a protein's function, and a key determinant for the production yield of a …

NetSolP: predicting protein solubility in Escherichia coli using language models

V Thumuluri, HM Martiny, JJ Almagro Armenteros… - …, 2022 - academic.oup.com
Motivation Solubility and expression levels of proteins can be a limiting factor for large-scale
studies and industrial production. By determining the solubility and expression directly from …

A descriptor set for quantitative structure‐property relationship prediction in biologics

K Sankar, K Trainor, LL Blazer, JJ Adams… - Molecular …, 2022 - Wiley Online Library
There has been a remarkable increase in the number of biologics, especially monoclonal
antibodies, in the market over the last decade. In addition to attaining the desired binding to …

PLM_Sol: predicting protein solubility by benchmarking multiple protein language models with the updated Escherichia coli protein solubility dataset

X Zhang, X Hu, T Zhang, L Yang, C Liu… - Briefings in …, 2024 - academic.oup.com
Protein solubility plays a crucial role in various biotechnological, industrial, and biomedical
applications. With the reduction in sequencing and gene synthesis costs, the adoption of …

AlphaFold 2-based stacking model for protein solubility prediction and its transferability on seed storage proteins

H Kwon, Z Du, Y Li - International Journal of Biological Macromolecules, 2024 - Elsevier
Accurate protein solubility prediction is crucial in screening suitable candidates for food
application. Existing models often rely only on sequences, overlooking important structural …