ASpdb: An Integrative Knowledgebase of Human Protein Isoforms From Experimental and AI-Predicted Structures

Authors

Yuntao Yang
Himansu Kumar
Yuhan Xie
Zhao Li
Rongbin Li
Wenbo Chen
Chiamaka S Diala
Meer A Ali
Yi Xu
Albon Wu
Sayed-Rzgar Hosseini
Erfei Bi
Hongyu Zhao
Pora Kim
W Jim Zheng

Publication Date

1-6-2025

Journal

Nucleic Acids Research

Abstract

Alternative splicing is a crucial cellular process in eukaryotes, enabling the generation of multiple protein isoforms with diverse functions from a single gene. To better understand the impact of alternative splicing on protein structures, protein-protein interaction and human diseases, we developed ASpdb (https://biodataai.uth.edu/ASpdb/), a comprehensive database integrating experimentally determined structures and AlphaFold 2-predicted models for human protein isoforms. ASpdb includes over 3400 canonical isoforms, each represented by both experimentally resolved and predicted structures, and >7200 alternative isoforms with AlphaFold 2 predictions. In addition to detailed splicing events, 3D structures, sequence variations and functional annotations, ASpdb uniquely offers comparative analyses and visualization of structural alterations among isoforms. This resource is invaluable for advancing research in alternative splicing, structural biology and disease mechanisms.

Keywords

Humans, Protein Isoforms, Alternative Splicing, Databases, Protein, Knowledge Bases, Protein Conformation, Models, Molecular, Molecular Sequence Annotation

DOI

10.1093/nar/gkae1018

PMID

39530217

PMCID

PMC11701669

PubMedCentral® Posted Date

11-12-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes