Fast and accurate protein intrinsic disorder prediction by using a pretrained language model

Y Song, Q Yuan, S Chen, K Chen… - Briefings in …, 2023 - academic.oup.com
Determining intrinsically disordered regions of proteins is essential for elucidating protein
biological functions and the mechanisms of their associated diseases. As the gap between …

The origin and structural evolution of de novo genes in Drosophila

J Peng, L Zhao - Nature Communications, 2024 - nature.com
Recent studies reveal that de novo gene origination from previously non-genic sequences is
a common mechanism for gene innovation. These young genes provide an opportunity to …

Critical assessment of protein intrinsic disorder prediction (CAID)‐Results of round 2

AD Conte, M Mehdiabadi, A Bouhraoua… - Proteins: Structure …, 2023 - Wiley Online Library
Protein intrinsic disorder (ID) is a complex and context‐dependent phenomenon that covers
a continuum between fully disordered states and folded states with long dynamic regions …

[HTML][HTML] SETH predicts nuances of residue disorder from protein embeddings

D Ilzhöfer, M Heinzinger, B Rost - Frontiers in Bioinformatics, 2022 - frontiersin.org
Predictions for millions of protein three-dimensional structures are only a few clicks away
since the release of AlphaFold2 results for UniProt. However, many proteins have so-called …

Digging into the 3D structure predictions of AlphaFold2 with low confidence: disorder and beyond

A Bruley, JP Mornon, E Duprat, I Callebaut - Biomolecules, 2022 - mdpi.com
AlphaFold2 (AF2) has created a breakthrough in biology by providing three-dimensional
structure models for whole-proteome sequences, with unprecedented levels of accuracy. In …

Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective

H Pei, W Guo, Y Peng, H Xiong… - Medicinal Research …, 2022 - Wiley Online Library
The key proteins involved in transcriptional regulation play convergent roles in cellular
homeostasis, and their dysfunction mediates aberrant gene expressions that underline the …

Ferritin self-assembly, structure, function, and biotechnological applications

VV Sudarev, SM Dolotova, SM Bukhalovich… - International journal of …, 2023 - Elsevier
Ferritin is a vital protein complex responsible for storing iron in almost all living organisms. It
plays a crucial role in various metabolic pathways, inflammation processes, stress response …

Deep learning in prediction of intrinsic disorder in proteins

B Zhao, L Kurgan - Computational and Structural Biotechnology Journal, 2022 - Elsevier
Intrinsic disorder prediction is an active area that has developed over 100 predictors. We
identify and investigate a recent trend towards the development of deep neural network …

Evaluation of AlphaFold structure-based protein stability prediction on missense variations in cancer

H Keskin Karakoyun, ŞK Yüksel, I Amanoglu… - Frontiers in …, 2023 - frontiersin.org
Identifying pathogenic missense variants in hereditary cancer is critical to the efforts of
patient surveillance and risk-reduction strategies. For this purpose, many different gene …

Bioinformatic analysis of lytic polysaccharide monooxygenases reveals the pan-families occurrence of intrinsically disordered C-terminal extensions

KC Tamburrini, N Terrapon, V Lombard, B Bissaro… - Biomolecules, 2021 - mdpi.com
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by
many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of …