CATH v4.4: major expansion of CATH by experimental and predicted structural data

BeStSel: analysis site for protein CD spectra-2025 update

Circular dichroism (CD) spectroscopy is a widely used technique to characterize the secondary structure composition of proteins. We have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which solves the main problem of protein CD spectroscopy-namely, the spectral variability of β-structures. The BeStSel web server utilizes this method to provide tools to the community for CD spectrum analysis. BeStSel uniquely provides information on eight secondary structure components, including parallel β-structure and antiparallel β-sheets with three different twist groups. It outperforms all available methods in accuracy and information content, and is also able to predict protein folds down to the topology/homology level of the CATH classification. The algorithm has been further developed, and the accuracy of the estimation of the secondary structure elements is improved by 0.7% as an average on the reference dataset. A new module of the web server calculates protein stability from the thermal denaturation profile followed by CD. Secondary structure calculations of uploaded PDB and mmcif files support the experimental verification of MD simulations and AlphaFold models by CD spectroscopy. Well-proven modules for disorder-order classification and extinction coefficient calculation continue to work. The BeStSel server is freely accessible at https://bestsel.elte.hu.

The 2025 Nucleic Acids Research database issue and the online molecular biology database collection

The 2025 Nucleic Acids Research database issue contains 185 papers spanning biology and related areas. Seventy three new databases are covered, while resources previously described in the issue account for 101 update articles. Databases most recently published elsewhere account for a further 11 papers. Nucleic acid databases include EXPRESSO for multi-omics of 3D genome structure (this issue's chosen Breakthrough Resource and Article) and NAIRDB for Fourier transform infrared data. New protein databases include structure predictions for human isoforms at ASpdb and for viral proteins at BFVD. UniProt, Pfam and InterPro have all provided updates: metabolism and signalling are covered by new descriptions of STRING, KEGG and CAZy, while updated microbe-oriented databases include Enterobase, VFDB and PHI-base. Biomedical research is supported, among others, by ClinVar, PubChem and DrugMAP. Genomics-related resources include Ensembl, UCSC Genome Browser and dbSNP. New plant databases cover the Solanaceae (SolR) and Asteraceae (AMIR) families while an update from NCBI Taxonomy also features. The Database Issue is freely available on the Nucleic Acids Research website (https://academic.oup.com/nar). At the NAR online Molecular Biology Database Collection (http://www.oxfordjournals.org/nar/database/c/), 932 entries have been reviewed in the last year, 74 new resources added and 226 discontinued URLs eliminated bringing the current total to 2236 databases.