Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

Motivation: Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome.

Results: We introduce a novel pairwise structure alignment tool (rcsb.

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins.

Recent advances in Artificial Intelligence and Machine Learning (., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information.

Reproducible Speech Research With the Artificial Intelligence-Ready PERCEPT Corpora.

Background: Publicly available speech corpora facilitate reproducible research by providing open-access data for participants who have consented/assented to data sharing among different research teams. Such corpora can also support clinical education, including perceptual training and training in the use of speech analysis tools.

Purpose: In this research note, we introduce the PERCEPT (Perceptual Error Rating for the Clinical Evaluation of Phonetic Targets) corpora, PERCEPT-R (Rhotics) and PERCEPT-GFTA (Goldman-Fristoe Test of Articulation), which together contain over 36 hr of speech audio (> 125,000 syllable, word, and phrase utterances) from children, adolescents, and young adults aged 6-24 years with speech sound disorder (primarily residual speech sound disorders impacting /ɹ/) and age-matched peers.

Endothelial PHACTR1 Promotes Endothelial Activation and Atherosclerosis by Repressing PPARγ Activity Under Disturbed Flow in Mice.

Background: Numerous genome-wide association studies revealed that SNPs (single nucleotide polymorphisms) at the (phosphatase and actin regulator 1) locus strongly correlate with coronary artery disease. However, the biological function of PHACTR1 remains poorly understood. Here, we identified the proatherosclerotic effect of endothelial PHACTR1, contrary to macrophage PHACTR1.