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09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
HDAPD: a web tool for searching the disease-associated protein structures
Yi-Ruen Lin1, Hsin-Yuan Wei, Tsung-Lin Tsai
1Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, HsinChu, 30013, Taiwan, Republic of China.
BMC Bioinformatics
|February 18, 2010
Summary
The HDAPD database allows direct searching of disease-associated protein structures by disease name, aiding structure-based drug design. This resource facilitates research into protein roles in disease development.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein structures are crucial for structure-based drug design against diseases.
- Current methods often rely on PDB IDs or sequence information for protein structure retrieval.
- A direct search by disease name for disease-associated proteins is lacking.
Purpose of the Study:
- To introduce the Human Disease Associated Protein (HDAP) database.
- To provide a user-friendly platform for accessing disease-associated protein structures.
- To support structure-based drug design efforts.
Main Methods:
- Developed the HDAPD database using a PHP-MySQL web interface.
- Implemented search functionality by disease name, protein name, type, or PDB ID.
- Integrated Jmol for 3D structure visualization, FASTA format for BLAST, and links to Gene Ontology (GO) and KEGG pathways.
Main Results:
- HDAPD enables direct searching of disease-associated protein structures via disease names.
- The database provides protein sequences in FASTA format for BLAST searches.
- Integrated data includes structural visualization, gene ontology, pathway information, and literature links.
Conclusions:
- The HDAPD database is a valuable, routinely updated resource for researchers.
- It facilitates the identification of disease-associated proteins for structure-based drug design.
- The database supports the investigation of protein roles in disease development and therapeutic strategies.
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