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CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated
Experimental Data on Protein and Peptide Aggregation
#MMPMID27043825
Thangakani AM
; Nagarajan R
; Kumar S
; Sakthivel R
; Velmurugan D
; Gromiha MM
PLoS One
2016[]; 11
(4
): e0152949
PMID27043825
show ga
Accurate distinction between peptide sequences that can form amyloid-fibrils or
amorphous ?-aggregates, identification of potential aggregation prone regions in
proteins, and prediction of change in aggregation rate of a protein upon
mutation(s) are critical to research on protein misfolding diseases, such as
Alzheimer's and Parkinson's, as well as biotechnological production of protein
based therapeutics. We have developed a Curated Protein Aggregation Database
(CPAD), which has collected results from experimental studies performed by
scientific community aimed at understanding protein/peptide aggregation. CPAD
contains more than 2300 experimentally observed aggregation rates upon mutations
in known amyloidogenic proteins. Each entry includes numerical values for the
following parameters: change in rate of aggregation as measured by fluorescence
intensity or turbidity, name and source of the protein, Uniprot and Protein Data
Bank codes, single point as well as multiple mutations, and literature citation.
The data in CPAD has been supplemented with five different types of additional
information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous
?-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different
lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are
available in the Protein Data Bank (PDB) and (v) Experimentally validated
aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is
linked to other related databases and resources, such as Uniprot, Protein Data
Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with
different search and display options so that users have the ability to get the
data in multiple ways. CPAD is freely available at
http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also
been discussed.
free
free
free
