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AmypDB Help

AMYPdb is a database dedicated to amyloid precursor proteins, and to the large scale signature analysis of those proteins. Its origin and goals are explained in the page "The AMYPdb Project", while the page "Amyloid Proteins" provides a rapid presentation of amyloid, amyloidosis and amyloid proteins families.

Table of contents :

Browsing amyloid precursor families

The "Protein Families" menu on the left provides rapid access to either recapitulative tables of amyloid and/or prion proteins, or to detailed informations regarding each amyloid protein family.

The "Description" page

It offers a quick overview of functions and pathologies related to the amyloid proteins, as well as a summary of the sequences listed in AMYPdb.Users can contribute to the description of the families using the link at their disposal. Links to Wikipedia entries are provided in several cases.

The "Proteins" page

It lists all known proteins for each amyloid family, in a table showing :
  • the entry name of the protein, linking to the corresponding UniProtKB entry
  • the description of the protein
  • the organism in wich the protein was identified, linking to the corresponding NCBI's Taxonomy Browser entry
  • the sequence length
  • the 3D structure(s), linking to the corresponding PDB entry
This table can be sorted by entry name, description, organisme and sequence length. Proteins can be selected to be exported in the FASTA format. Registered users can also add proteins to their working sets (see below).

The "Alignment" page

It offers access to multiple aligment(s) of amyloid proteins, using the JalView applet. It requires Java to be installed on the user's computer.

The "Patterns" page

It gives access to several list of AMYPdb patterns matching each amyloid family :
  • patterns classified by correlation coefficient
  • patterns originating from PROSITE
  • patterns also found in other amyloid families, classified by correlation coefficient
Each list of patterns is ordered by correlation, sensiticity and specificity, and displays the same patterns informations :
  • the pattern, linking to a more detailed description
  • quality parameters : correlation, sensitivity, specificity
  • pattern length
  • number of matching proteins
  • tool used for the discovery of the pattern, linking to its website
  • some of the parameters used for the pattern discovery
  • number of other amyloid families matching the pattern
  • number of non amyloid proteins matching the pattern
Each pattern has a detailed entry showing :
  • the pattern
  • quality parameters : correlation, sensitivity, specificity
  • pattern length
  • number of matching proteins
  • number of other amyloid families matching the pattern
  • number of non amyloid proteins matching the pattern : a "View sequences" link leads to a list of the corresponding sequences showing the highlighted pattern and its position in the sequence
  • proteins matching or not matching the pattern : a "View sequences" link leads to a list of the corresponding sequences showing the highlighted pattern and its position in the sequence
  • protein features at the pattern positions
  • other amyloid families matching the pattern, with quality parameters and sequences, and linking to the description of the pattern for those families, to the description of those families, and to the list of sequences matching the pattern
  • tool used for the discovery of the pattern, linking to its website
  • parameters used for the pattern discovery
  • data regarding the set of sequences used for the pattern discovery

The "3D Structures" page

It lists all known 3D structures known for proteins of each amyloid families, providing the following informations :
  • the entry name of the protein, linking to the corresponding UniProtKB entry
  • the description of the protein
  • the organism in wich the protein was identified, linking to the corresponding NCBI's Taxonomy Browser entry
  • the 3D structure, linking to the corresponding PDB entry
  • the 3D structure identifyer, linking to the corresponding PDB entry
  • a link to the corresponding article in the PDB
  • visualisation of the structure using MBT SimpleViewer and Jmol

The "Bibliography" page

It lists scientific publications regarding each amyloid family. Links to the corresponding entries in PubMed are provided.

The "Protein" page

Each protein sequence is summarized in a page showing:
  • the Uniprot Entry name of the protein
  • the name of the protein, and its aliases
  • the source of knowledge (SwissPort or TrEMBL)
  • the Amyloid Family to which the sequence is associated
  • the Label that define amyloid knowledge quality :
    LabelNumber of proteinsQuality rankDefinition
    Amyloid in vivo0
    		the precursor protein, or a specific sub-segment, forms fibrils in human, or animals, or is a yeast prion
    Amyloid in vitro0
    		the polypeptide forms fibrils under experimental conditions
    Amyloid in silico0
    		the polypeptide forms fibrils using computational techniques
    Putative amyloid protein0
    		the protein is a member of an amyloid family, but the amyloid properties of that specific member were not assessed
    Unclassified protein0
    		the protein family does not fulfill the definition of amyloid, but sparse data show that at least one member of the family shares some amyloid properties
  • the organism in wich the protein was identified, linking to the corresponding NCBI's Taxonomy Browser entry
  • the SwissProt keywords
  • the 3D structure(s), linking to the corresponding PDB entry
  • all the patterns matching with the sequence (click to show pattern list)
  • the sequence in FASTA format (by clicking on the length), and if it is a fragment
  • the comments from Experts
  • all publications from PubMed on the protein sequence
By clicking on icon, 'Label' field and 'Experts Comments' aera can be modified using an Expert account (register and contact us by email)

In-depth data manipulation with AMYPdb

The search engine

  • Free Text Search : search for keywords in the description of amyloid families, articles and protein sequences.
  • Pattern Matching with Amyloid Sequences : search for amyloid proteins matching a given pattern
  • Sequence Matching with Amyloid Patterns : search for AMYPdb patterns matching a given protein sequence
  • Advanced Pattern Search : search for patterns matching given quality parameters (sensitivity, specificity and/or correlation) for the selected family(ies)
  • Protein Search : check if a protein is stored in AMYPdb, given its UniProtKB accession number
  • Pattern Search : check if a pattern is stored in AMYPdb, given its PROSITE accession number or by entering the pattern in PROSITE format

The working sets

Visitors can freely create a user account using the menu at the bottom left. It will allow them to access the working set functions, via a new menu on the left. Working sets are private workspaces allowing users to manage their own datasets of proteins. Proteins can be selected in the "Proteins" page of amyloid families. They also can be easily moved from one dataset to another, exported in FASTA format, and deleted from the working sets.

Computation on proteic sequences

These menus allow visitors to submit proteic sequences in FASTA format to compute profiles for differents aggregation predictors or amino acid parameters.

The Prediction page

This page gives access to different aggregation prediction methods.

The Calculation page