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Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data
(Springer, 2019-05)
Major histocompatibility complex (MHC) class II antigen presentation is a key component in eliciting a CD4+ T cell response. Precise prediction of peptide-MHC (pMHC) interactions has thus become a cornerstone in defining ...
Footprints of antigen processing boost MHC class II natural ligand predictions
(Springer Nature, 2018-11)
BACKGROUND: Major histocompatibility complex class II (MHC-II) molecules present peptide fragments to T cells for immune recognition. Current predictors for peptide to MHC-II binding are trained on binding affinity data, ...
Determination of a predictive cleavage motif for eluted major histocompatibility complex class II ligands
(Frontiers Media S.A., 2018-08)
CD4+ T cells have a major role in regulating immune responses. They are activated by recognition of peptides mostly generated from exogenous antigens through the major histocompatibility complex (MHC) class II pathway. ...
Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data
(American Chemical Society, 2018-01)
Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules ...
CALI: a novel model for visual mining of biological relevant patterns in protein-ligand graphs
(Universidade Federal de Minas GeraisBrasilICX - DEPARTAMENTO DE CIÊNCIA DA COMPUTAÇÃOPrograma de Pós-Graduação em Ciência da ComputaçãoUFMG, 2016-10-27)
Protein-ligand interaction (PLI) networks show how proteins interact with small nonprotein
ligands and can be used to study molecular recognition, which plays an important
role in biological systems. The binding and ...
AFAL: a web service for profiling amino acids surrounding ligands in proteins
(2014)
With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the ...
Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions
(American Chemical Society, 2017-04)
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has ...