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APR Prediction Models
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
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Tutorial
Statistics
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APR Prediction Models:
GAP (Generalized Aggregation Proneness)
ANuPP (Prediciton of Nucleating APRs)
V
L
AmY-Pred (Predicting antibody light chain aggregation)
Aggregation Kinetics Prediction Models:
AggreRATE-Disc (Classifying Aggregating Point Mutation)
AggreRATE-Pred (Predicting Aggregation Rate for Point Mutation)
AbsoluRATE (Predicting Absolute aggregation rate)
Amylo-Pipe (Comprehensive aggregation prediction)
statistics of the database
Amyloid Proteins and Peptide Dataset
Information
CPAD
CPAD 2.0
Dataset size
Redundant data points: Amyloid hexapeptides (GAP): 179, Amyloid hexapeptides (Waltz-DB ): 244, Amyloid peptides (different length): 332, Amorphous peptides (GAP): 168, Non-amyloid peptides (Waltz-DB): 845
Total data points: 2031 (from GAP, AmyLoad, Waltz-DB 2.0) Amyloid-forming peptides (all length): 917 Non-amyloid peptides: 1114
Related information
None
Information on source protein with literature information (if available)
Derived properties
None
Calculated aggregation related properties for the peptides such as Net charge, Absolute charge, Hydrophobic residue percentage, Gatekeepers and position of peptide in source protein, Aggregation propensity from various servers, the orientation of fibrils (from PASTA server)
The data collected to develop GAP server (by Protein Bioinformatics Lab) has been merged with the CPAD database in current version. The source of all entries from GAP will be marked as CPAD.
Aggregation-prone regions (APRs) in amyloidogenic proteins
Information
CPAD
CPAD 2.0
Dataset size
33 Unique proteins
268 unique proteins, 912 APRs information
APR information
Protein name, Protein sequence, Position of APR, APR sequence, Reference
APR information
(Length, Mutation(s), APR sequence)
Protein information
(Protein Name, Species, UniProt ID, Uniprot Name, PDB ID, Catagory (Pathogenic, Functional), Prion Information, Protein sequence, APR position in the sequence with gatekeeper information)
Literature information
(Pubmed link, PMID, Source database)
Aggregation Kinetics database
Information
CPAD
CPAD 2.0
Database size
2356 data on the change in aggregation rate upon mutation
collectively 83098 data on experimental aggregation rate (We have merged the intensity (time kinetics) values for each experiment for better representation and plotting)
82066 data points on time kinetics were merged into 1781 records.
(refer to time kinetics database or tutorial)
Objective of the database
To collect the experimental information on point mutation
To collect the experimental information on any kind of aggregation data The dataset is divided into 3 parts:
(1)
Aggregation rate: The aggregation rate already calculated in the literature by fitting the curve
(2)
Intensity (Time kinetics): The time-dependent experimental aggregation kinetics data (mostly with characteristics sigmoidal curve)
(3)
Intensity (Other): The experimental aggregation experiments performed under varying experimental condition. (observations made at either equilibrium or Max fluorescence)
Other stats
Wild-type data: 586 Point mutation data: 1658
Wild-type data: 40555 Point mutation data: 39608 Double mutation data: 1293 triple mutation data: 169 Multiple mutation data: 866 Modified residue mutation data: 613
Structure of Aggregating Proteins
Information
CPAD
CPAD 2.0
Dataset size
Does not contain structure information (However, 23 amyloid peptides with known structures were mentioned in CPAD)
Contains 565 data with PDB information in the following sub-category:
(1)
Peptides: 42 structures
(2)
Protein: 159 structures
(3)
Fibrils: 215 structures
(4)
Aggregating complex (with ligand): 14 structures
(5)
Inhibitor complex (with ligand): 130 structures
(6)
Fibril complex: 2 structures
(7)
Protein complex: 3 structures
There is also a separate categorization: amyloid and non-amyloid structures
Structure information
No information available other than PDB ID
Protein information: (Protein Name, Species, Uniprot ID, PDB ID, Length, Mutation(s), Protein sequence) Structure information: (PDB Structure, Secondary Structure, Experimental method to determine the structure, Resolution, R-value Free, PDB classification, Global Stoichiometry, Ligand information, Contact map Literature information: Pubmed link, Author, PMID