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AMYPdb: A database dedicated to amyloid precursor proteins
Abstract Background: Misfolding and aggregation of 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. Conclusion: 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].interest. AMYPdb is freely accessible [1].
Abstractsub Background: Misfolding and aggregation of 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. Conclusion: 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].interest. AMYPdb is freely accessible [1].
Bibtextype article  +
Doi 10.1186/1471-2105-9-273  +
Has author Pawlicki S. + , Le Bechec A. + , Delamarche C. +
Has extra keyword Amino acid sequence + , Amyloid precursor proteins + , Bibliographic references + , Collaboration environments + , Conformational change + , Fibrillar structures + , Large-scale sequences + , Molecular mechanism + , Amino acids + , Bibliographic retrieval systems + , Bioinformatics + , Database systems + , Glycoproteins + , Neurodegenerative diseases + , Proteins + , Alpha fibrinogen + , Alpha synuclein + , Amylin + , Amyloid A protein + , Amyloid beta protein + , Amyloid precursor protein + , Apolipoprotein A1 + , Atrial natriuretic factor + , Beta 2 microglobulin + , Calcitonin + , Cystatin C + , Fibrinogen + , Gelsolin + , Glycoprotein + , Huntingtin + , Immunoglobulin + , Insulin + , Lactadherin + , Lysozyme + , Parkin + , Polypeptide + , Prealbumin + , Prion protein + , Prolactin + , Protein C + , Protein het s + , Protein New 1 + , Serine proteinase inhibitor + , Tau protein + , Access to information + , AMYPdb + , Article + , Automated pattern recognition + , Bibliographic database + , Computer analysis + , Computer program + , Data synthesis + , Information processing + , Online system + , Protein aggregation + , Protein analysis + , Protein database + , Protein folding + , Proteomics + , Sequence analysis + , Animal + , Central nervous system disease + , Chemistry + , Diabetes mellitus + , Genetics + , Human + , Metabolism + , Molecular genetics + , Sequence homology + , Amino Acid Sequence + , Amyloid beta-Protein Precursor + , Animals + , Central Nervous System Diseases + , Databases + , Protein + , Diabetes Complications + , Humans + , Molecular Sequence Data + , Protein Folding + , Sequence Homology + , Amino Acid +
Issn 14712105  +
Language English +
Number of citations by publication 0  +
Number of references by publication 0  +
Published in BMC Bioinformatics +
Pubmed 18544157  +
Title AMYPdb: A database dedicated to amyloid precursor proteins +
Type journal article  +
Volume 9  +
Year 2008 +
Creation dateThis property is a special property in this wiki. 6 November 2014 13:28:10  +
Categories Publications without keywords parameter  + , Publications without license parameter  + , Publications without remote mirror parameter  + , Publications without archive mirror parameter  + , Publications without paywall mirror parameter  + , Journal articles  + , Publications without references parameter  + , Publications  +
Modification dateThis property is a special property in this wiki. 6 November 2014 13:28:10  +
DateThis property is a special property in this wiki. 2008  +
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