dbPTM: an information repository of protein post-translational modification.
dbPTM is a database that compiles information on protein post-translational modifications (PTMs), such as the catalytic sites, solvent accessibility of amino acid residues, protein secondary and tertiary structures, protein domains and protein variations. The database includes all of the experimentally validated PTM sites from Swiss-Prot, PhosphoELM and O-GLYCBASE. Only a small fraction of Swiss-Prot proteins are annotated with experimentally verified PTM. Although the Swiss-Prot provides rich information about the PTM, other structural properties and functional information of proteins are also essential for elucidating protein mechanisms. The dbPTM systematically identifies three major types of protein PTM (phosphorylation, glycosylation and sulfation) sites against Swiss-Prot proteins by refining our previously developed prediction tool, KinasePhos (http://kinasephos.mbc.nctu.edu.tw/). Solvent accessibility and secondary structure of residues are also computationally predicted and are mapped to the PTM sites. The resource is now freely available at http://dbPTM.mbc.nctu.edu.tw/.
Lee
Tzong-Yi
TY
Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan.
Huang
Hsien-Da
HD
Hung
Jui-Hung
JH
Huang
Hsi-Yuan
HY
Yang
Yuh-Shyong
YS
Wang
Tzu-Hao
TH
D000596:Amino Acids / Q000737:chemistry; D003196:Computer Graphics; D030562:Databases, Protein / Q000706:statistics & numerical data; D006031:Glycosylation; D020407:Internet; D010766:Phosphorylation; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface
D000596:Amino Acids; D011506:Proteins