HDAPD: a web tool for searching the disease-associated protein structures.
BACKGROUND
The protein structures of the disease-associated proteins are important for proceeding with the structure-based drug design to against a particular disease. Up until now, proteins structures are usually searched through a PDB id or some sequence information. However, in the HDAPD database presented here the protein structure of a disease-associated protein can be directly searched through the associated disease name keyed in.


METHODS
The search in HDAPD can be easily initiated by keying some key words of a disease, protein name, protein type, or PDB id. The protein sequence can be presented in FASTA format and directly copied for a BLAST search. HDAPD is also interfaced with Jmol so that users can observe and operate a protein structure with Jmol. The gene ontological data such as cellular components, molecular functions, and biological processes are provided once a hyperlink to Gene Ontology (GO) is clicked. Further, HDAPD provides a link to the KEGG map such that where the protein is placed and its relationship with other proteins in a metabolic pathway can be found from the map. The latest literatures namely titles, journals, authors, and abstracts searched from PubMed for the protein are also presented as a length controllable list.


CONCLUSIONS
Since the HDAPD data content can be routinely updated through a PHP-MySQL web page built, the new database presented is useful for searching the structures for some disease-associated proteins that may play important roles in the disease developing process for performing the structure-based drug design to against the diseases.
Lin
Yi-Ruen
YR
Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, HsinChu, 30013, Taiwan, Republic of China.
Wei
Hsin-Yuan
HY
Tsai
Tsung-Lin
TL
Lin
Thy-Hou
TH
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins