PhyreRisk

Release Information:

Features:

Generated and added Phyre models (where possible) for proteins with sequence length greater than 2500

Improvements / Issues Resolved:

Known Issues:

3DMol viewer does not allow loading of compressed structure coordinate files - experimental structure from PDB are downloaded in a compressed format for performance and efficiency
Sometimes sequence <=> structure mappings are not generated for some experimental structures due to SIFTS mapping not being available - in such cases sequence <=> structure colouring and communication cannot be applied
Sometimes colour transfer does not happen due to race conditions (in other words, when the colour commands are generated and applied prematurely as a result of a structure being downloaded / loaded slower in Jsmol). This is dependent on a lot of factors such as the structure file size, internet connectivity speed, client machine processor speed, client machine browser speed etc.

Release Information:

Features:

Scripting of interactivity for the JSMol molecular viewer
Implementation of a ranked graphical structure selection viewer
Ability to visualise location of variants in sequence & structure (for both standard and user-supplied variants)
Ability to download all available structural data (experimental & predicted)
Implemented ability to store/remember user settings / view state
Implementation/publishing of RESTful Web-Service API end-points for interoperability
Developed and enabled interactive guided tutorial using intro.js library
Implementation of GDPR requirement
Added abililty to search by Isoform Id, Ensembl Transcript, Gene or Protein Ids

Improvements / Issues Resolved:

Updated JsMol (14.29.29)
PhyreRisk database enhancement to accommodate additional data requirements
Added 22,271 alternative protein sequences (Isoforms) from UniProt to PhyreRisk database
Fixed bug preventing NGLViewer and 3DMol molecular viewer from rendering
Enabled Google analytics tracking
Added Plain and Structure type colour scheme to the sequence viewer
Modified legend for 'Structure Selection' section. Selected structure now has a black boarder
Updated default examples for 'Genetic' & 'Protein' variant(s) input page
Provided a button to enable manual triggering of structure colour transfer to Jsmol viewer when it does not happen automatically due to race conditions

Known Issues:

3DMol viewer does not allow loading of compressed structure coordinate files - experimental structure from PDB are downloaded in a compressed format for performance and efficiency
Sometimes sequence <=> structure mappings are not generated for some experimental structures due to SIFTS mapping not being available - in such cases sequence <=> structure colouring and communication cannot be applied
Sometimes colour transfer does not happen due to race conditions (in other words, when the colour commands are generated and applied prematurely as a result of a structure being downloaded / loaded slower in Jsmol). This is dependent on a lot of factors such as the structure file size, internet connectivity speed, client machine processor speed, client machine browser speed etc.

Release Information:

Features:

Ability to search PhyreRisk database using UniProt accession, protein name, gene name and disease name
Addition of experimentally derived structures of human proteins from ePDB at EBI
Integration of three molecular viewers (JSMol, 3DMol, NGLViewer)
Integration of SIFTS resource provided by EBI to enable mapping and linking of sequence from UniProt with structure coordinates from PDB
Integration of VEP rest service
Provided ability to input custom variant using genomic coordinates (human build GRCh37 or GRCh38)
Provided ability to add custom variants using protoemic coordinates

Improvements / Issues Resolved:

Updated PhyreRisk database with 20,349 reviewed human proteins from UniProt (Nov 2018)
Resolved bug that prevents JSMol from loading PDB coordinate files containing disulphide bonds (SSBOND)
Added google map and address on contact page
Resolved bug preventing search on the protein page

Known Issues:

3DMol viewer does not load compressed structure coordinate file - experimental structure from PDB are downloaded in a compressed format for performance and efficiency

Release Information:

Features:

Initial design and development PhyreRisk database
Population of PhyreRisk database with 20,214 reviewed human proteins from UniProt
Initial responsive user interface design using mobile first approach
PhyreRisk branding (Logo / favicon design, Colour scheme development, CSS design)
Design and implementation of Web Alignment Viewer JavaScript (WaveJS) for visualising single protein sequences
Integration of WaveJS (our in-house custom sequence viewer)

Improvements / Issues Resolved:

Known Issues: