pHLA3D: An online database of predicted three-dimensional structures of HLA molecules
| Autor: | Semiramis Jamil Hadad do Monte, Mário Sérgio Coelho Marroquim, Ricardo Martins Ramos, Jhonatan Matheus Sousa Costa, Antonio Gilberto Borges Coelho, Rafael Melo Santos de Serpa Brandão, Deylane Menezes Teles e Oliveira, Adalberto Socorro da Silva, Luiz Claudio Demes da Mata Sousa, Francisco das Chagas Alves Lima, Antonio Vanildo de Sousa Lima |
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| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular 0301 basic medicine Computer science Immunology Human leukocyte antigen Computational biology Web Browser computer.software_genre Protein Structure Secondary Epitope Epitopes 03 medical and health sciences 0302 clinical medicine Hla molecules Humans Immunology and Allergy Amino Acid Sequence Databases Protein Alleles Web application framework Histocompatibility Antigens Class I Online database MODELLER General Medicine 030104 developmental biology Template Structural Homology Protein Histocompatibility Database Management Systems Solid organ transplantation computer 030215 immunology |
| Zdroj: | Human Immunology. 80:834-841 |
| ISSN: | 0198-8859 |
| DOI: | 10.1016/j.humimm.2019.06.009 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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