The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …

InterPro: the protein sequence classification resource in 2025<? mode longmeta?>

M Blum, A Andreeva, LC Florentino… - Nucleic Acids …, 2025 - academic.oup.com
Abstract InterPro (https://www. ebi. ac. uk/interpro) is a freely accessible resource for the
classification of protein sequences into families. It integrates predictive models, known as …

De novo design of knotted tandem repeat proteins

LA Doyle, B Takushi, RD Kibler, LF Milles… - Nature …, 2023 - nature.com
De novo protein design methods can create proteins with folds not yet seen in nature. These
methods largely focus on optimizing the compatibility between the designed sequence and …

Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution

X Xiao, CY Zhang, Z Zhang, Z Hu, M Li, T Li - Molecular Psychiatry, 2022 - nature.com
Genome-wide association studies (GWASs) have revealed substantial genetic components
comprised of single nucleotide polymorphisms (SNPs) in the heritable risk of psychiatric …

Diversity and features of proteins with structural repeats

EI Deryusheva, AV Machulin, OV Galzitskaya - Biophysical Reviews, 2023 - Springer
The review provides information on proteins with structural repeats, including their
classification, characteristics, functions, and relevance in disease development. It explores …

The Pfam protein families database: embracing AI/ML

T Paysan-Lafosse, A Andreeva, M Blum… - Nucleic Acids …, 2025 - academic.oup.com
The Pfam protein families database is a comprehensive collection of protein domains and
families used for genome annotation and protein structure and function analysis …

[HTML][HTML] Deep learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space

S Mesdaghi, RM Price, J Madine, DJ Rigden - Journal of Structural Biology, 2023 - Elsevier
Repeat proteins are common in all domains of life and exhibit a wide range of functions. One
class of repeat protein contains solenoid folds where the repeating unit consists of β-strands …

STRPsearch: fast detection of structured tandem repeat proteins

S Mozaffari, PN Arrías, D Clementel, D Piovesan… - …, 2024 - academic.oup.com
Abstract Motivation Structured Tandem Repeats Proteins (STRPs) constitute a subclass of
tandem repeats characterized by repetitive structural motifs. These proteins exhibit distinct …

RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB

D Clementel, PN Arrías, S Mozaffari… - Nucleic Acids …, 2025 - academic.oup.com
Abstract RepeatsDB (URL: https://repeatsdb. org) stands as a key resource for the
classification and annotation of Structured Tandem Repeat Proteins (STRPs), incorporating …

The difference in structural states between canonical proteins and their isoforms established by proteome-wide bioinformatics analysis

Z Osmanli, T Falgarone, T Samadova, G Aldrian… - Biomolecules, 2022 - mdpi.com
Alternative splicing is an important means of generating the protein diversity necessary for
cellular functions. Hence, there is a growing interest in assessing the structural and …