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Updated: Jun 7, 2025
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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures
Yuntao Yang1, Himansu Kumar1, Yuhan Xie2
1McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Suite 600, Houston, TX 77030, USA.
Nucleic Acids Research
|November 12, 2024
Summary
Alternative splicing generates diverse protein isoforms. ASpdb is a new database offering structural insights into these isoforms, aiding research in splicing, structural biology, and diseases.
Area of Science:
- Molecular Biology
- Structural Biology
- Bioinformatics
Background:
- Alternative splicing is a key eukaryotic process generating protein diversity from single genes.
- Understanding splicing's impact on protein structure, interactions, and disease is crucial.
- Existing resources may lack comprehensive structural data for alternative splicing isoforms.
Purpose of the Study:
- To develop ASpdb, a database integrating experimental and predicted structures of human protein isoforms.
- To provide a resource for analyzing structural changes due to alternative splicing.
- To facilitate research into the functional and disease implications of alternative splicing.
Main Methods:
- Integrated experimentally determined protein structures.
- Incorporated AlphaFold 2-predicted models for protein isoforms.
- Developed comparative analyses and visualization tools for structural alterations.
Main Results:
- ASpdb contains >3400 canonical and >7200 alternative human protein isoforms.
- Each isoform is represented by both experimental and predicted 3D structures.
- The database includes splicing events, sequence variations, and functional annotations.
Conclusions:
- ASpdb offers a unique resource for studying alternative splicing at the structural level.
- The database supports research in structural biology, protein function, and human disease mechanisms.
- Comparative structural analysis of isoforms is facilitated by ASpdb.
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