AMYPdb: a database dedicated to amyloid precursor proteins.
BACKGROUND
Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases.


RESULTS
We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. It displays links to more than 2,300 bibliographic references and 1,200 3D-structures. A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. We generated and analyzed 3,621 amino acid sequence patterns, reporting highly specific patterns for each amyloid family, along with patterns likely to be involved in protein misfolding and aggregation.


CONCLUSIONS
AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely accessible 1.
Pawlicki
Sandrine
S
Université de Rennes I and CNRS UMR 6026, Equipe Structure et Dynamique des Macromolécules, Campus de Beaulieu, Nb 13, 35042 RENNES Cedex, France. sandrine.pawlicki@laposte.net
Le Béchec
Antony
A
Delamarche
Christian
C
D000595:Amino Acid Sequence; D016564:Amyloid beta-Protein Precursor / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D002493:Central Nervous System Diseases / Q000378:metabolism; D030562:Databases, Protein; D048909:Diabetes Complications; D006801:Humans; D008969:Molecular Sequence Data; D017510:Protein Folding; D017386:Sequence Homology, Amino Acid
D016564:Amyloid beta-Protein Precursor