[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

[HTML][HTML] Computational protein design with deep learning neural networks

J Wang, H Cao, JZH Zhang, Y Qi - Scientific reports, 2018 - nature.com
Computational protein design has a wide variety of applications. Despite its remarkable
success, designing a protein for a given structure and function is still a challenging task. On …

Computational tools help improve protein stability but with a solubility tradeoff

A Broom, Z Jacobi, K Trainor, EM Meiering - Journal of Biological Chemistry, 2017 - ASBMB
Accurately predicting changes in protein stability upon amino acid substitution is a much
sought after goal. Destabilizing mutations are often implicated in disease, whereas …

Novel function discovery through sequence and structural data mining

B Lobb, AC Doxey - Current opinion in structural biology, 2016 - Elsevier
Highlights•Homology detection remains essential for many function prediction
methods.•Homologs found in unexpected places may reveal profound functional …

Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

F Lapenta, J Aupič, M Vezzoli, Ž Strmšek… - Nature …, 2021 - nature.com
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of
polypeptide nanostructures. CCPO folds are defined by the sequential order of …

Crystal Structure of de Novo Designed Coiled-Coil Protein Origami Triangle

T Satler, S Hadži, R Jerala - Journal of the American Chemical …, 2023 - ACS Publications
Coiled-coil protein origami (CCPO) uses modular coiled-coil building blocks and topological
principles to design polyhedral structures distinct from those of natural globular proteins …

A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication

L Paladin, M Necci, D Piovesan, P Mier… - Journal of Structural …, 2020 - Elsevier
Abstract Tandem Repeat Proteins (TRPs) are ubiquitous in cells and are enriched in
eukaryotes. They contributed to the evolution of organism complexity, specializing for …

Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity

DM Anderson, LP Jayanthi, S Gosavi… - Frontiers in Molecular …, 2023 - frontiersin.org
Kinetic stability, defined as the rate of protein unfolding, is central to determining the
functional lifetime of proteins, both in nature and in wide-ranging medical and …

[PDF][PDF] 耐有机溶剂氨基酸脱氢酶基因挖掘与非天然氨基酸的非水相合成

段凌暄, 姚光晓, 江亮, 王世珍 - 化工学报, 2021 - hgxb.cip.com.cn
可在非水相体系高效催化不对称还原反应制备手性化合物的氧化还原酶具有重要科学意义与
工业应用前景. 基于基因挖掘技术, 获得了17 个耐盐氨基酸脱氢酶的基因 …

Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity

VY Zhao, JV Rodrigues, ER Lozovsky, DL Hartl… - Biophysical …, 2021 - cell.com
To what degree are individual structural elements within proteins modular such that similar
structures from unrelated proteins can be interchanged? We study subdomain modularity by …