title: DockTope: a Web-based tool for automated pMHC-I modelling.
abstract: The immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8(+) T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides), and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.
authors.forename: Maurício Menegatti
authors.initials: MM
authors.lastname: Rigo
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.|Department of Computer Science, Rice University, Houston, Texas, 77005, USA.
authors.forename: Dinler Amaral
authors.initials: DA
authors.lastname: Antunes
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.
authors.forename: Martiela
authors.initials: M
authors.lastname: Vaz de Freitas
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.
authors.forename: Marcus
authors.initials: M
authors.lastname: Fabiano de Almeida Mendes
authors.affiliation: CESUP-Centro Nacional de Supercomputação, Universidade Federal do Rio Grande do Sul, Postcode 90035-190, Brazil.
authors.forename: Lindolfo
authors.initials: L
authors.lastname: Meira
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.
authors.forename: Marialva
authors.initials: M
authors.lastname: Sinigaglia
authors.affiliation: Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Postcode 91501-970, Brazil.
authors.forename: Gustavo Fioravanti
authors.initials: GF
authors.lastname: Vieira
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D018414:CD8-Positive T-Lymphocytes / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D000939:Epitopes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D000072417:Protein Domains; D015203:Reproducibility of Results
chemical_list: D000939:Epitopes; D015395:Histocompatibility Antigens Class I; D010455:Peptides