Table 1.
Databases providing access to red blood cells gene and protein expression.
Table 2.
Category of 3D structural models and tools.
Table 3.
Schedules for data queries from reference databases, data processing and structural model prediction.
Fig 1.
Description of the enriched protein entry available in the RESPIRE database.
Aquaporin-1 protein (RESPIRE id: 641) serves as an example. (A) Protein name, amino acids length and molecular weight, as parsed from Uniprot. (B) Sequence details enriched with conserved position in the protein family, secondary structure representation in cartoon and amino acids co-evolution, color-coded from low conservation (blue) to high conservation (red) (see text for details). (C) Protein domains decomposition generated using InterProScan. (D) Protein structure interactive visualisation allowing to map the position of variants and mutants on the displayed molecule. (E) Binding partners mapping, with links to the corresponding entry in the database or to UNIPROT when required. (F) Gene Ontology annotations with links to all proteins related to this term in the database, and links to the Gene Ontology web site when the user wants to complete the definition. (G) Additional clinical and genetic information concerning the protein, as gathered with permissions from the OMIM database. (H) Profile of the protein profile expression during hematopoiesis. (I) History of the protein entry, with a complete trace of updates. (J) Indication of the protein detection in scientific literature.
Fig 2.
Details of protein structural content.
Each experimental structure or produced model is displayed at the top with a score to rank the more complete structures: first for experimental structures, and then the best model according to the modelling method internal score. Hovering on each entry name shows in a condensed view the experimental information or the model origin. By clicking on any entry presented, the corresponding PDB file is uploaded to the JSmol viewer for interactive manipulations. The more complete JSmol menu can be opened with a right-click on the JSmol canvas. A list of known variants is shown below the templates window, with a brief description and a link to the upstream description. By selecting a variation, the user will highlight on the structure the position of the amino acid mutation. (A) Detail of the structural interactive view for Aldo-keto reductase family 1 member C3. The mutation of a proline for a serine at position 180 is represented in brown sphere representation. (B) Detail of the CD59 glycoprotein entry. For this protein, there is no sufficient structural coverage available (indicated in orange, 62% only can be determined using structural experimental data), so a model was produced using I-TASSER [56,69,70]. This resulting model is considered an average model with a TM-Score of 0.62.
Fig 3.
RESPIRE can be accessed through various queries.
Example of precomputed requests. Clicking on the links will retrieve all proteins pertaining to a given category. (A) Query results concerning the “membrane” annotation in UNIPROT. 384 proteins are annotated with this membranous localisation. By clicking on a number or letter, the user can see all the protein names starting with this item, with an indication of an existing structural when the (3D) keyword is appended to the name, proteins starting with letter E are displayed. (B) By clicking on the button “Download the protein list”, the user will be provided a Comma Separated Value file containing the protein name, its identifier in RESPIRE and UNIPROT, the protein length, its structural status and its cellular localisation. (C) A close “plasma membrane” annotation can be accessed by clicking on the GO entry GO:0005886 in the statistics tab or in any entry possessing this annotation. This time 545 entries will be displayed and can also be retrieved. (D) To access rapidly to a protein using its name or description, it is possible to use the “search-as-you-type” facility provided at the top right in the menu, for instance to retrieve a member of the Solute Carrier Family.