ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures.

Journal: Nucleic acids research
PMID: 39530217

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.

Authors

  • Yuntao Yang
    School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, Texas, USA.
  • Himansu Kumar
    School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
  • Yuhan Xie
    School of Electronics and Communication Engineering, Sun Yat-sen University, Guangzhou, China.
  • Zhao Li
    Research Center for Data Hub and Security, Zhejiang Lab, Hangzhou, China. lzjoey@gmail.com.
  • Rongbin Li
    School of Biomedical Informatics, University of Texas Health Science Center at Houston; Yale University; Melax Technologies, Houston.
  • Wenbo Chen
    Polytechnic Institute, Zhejiang University, Hangzhou 310000, China.
  • Chiamaka S Diala
    McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States.
  • Meer A Ali
    McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Suite 600, Houston, TX 77030, USA.
  • Yi Xu
    School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.
  • Albon Wu
  • Sayed-Rzgar Hosseini
    School of Biomedical Informatics, University of Texas Health Science Center (UTHealth), Houston, TX, USA.
  • Erfei Bi
    Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Room 1156, BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA.
  • Hongyu Zhao
    SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; Department of Biostatistics, Yale University, New Heaven, USA.
  • Pora Kim
    Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
  • W Jim Zheng
    McWilliams School of Biomedical Informatics, University of Texas Health Science at Houston, Houston, TX, USA.

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