pHLA3D: An online database of predicted three-dimensional structures of HLA molecules

HLA epitope analysis emerged as a strategy to determine alloimmune risk in solid organ transplantation. However, it requires not only knowledge on HLA amino acids sequences, but also on HLA three-dimensional structures. Unfortunately, the number of structures available is still unsatisfactory. This work reports the modelling of 106 heterotrimeric (alpha chain + β₂M + peptide) HLA class I molecules. The models were generated by homology modelling using Modeller, refined using GalaxyRefine server, heterodimerized with Swiss-PDB Viewer and, finally, assessed as to their structural quality through Dali server. The final structures were made available through a free online database, pHLA3D (www.phla3d.com.br), developed in Ruby language using the Ruby on Rails web framework. Structural parameters were similar between refined molecules and their templates. The new database may improve HLA epitope analysis and better guide risk assessment in solid organ transplantation setting.