Research article
Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
-
* Corresponding author: Bjoern Peters bpeters@liai.org
1 Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
2 Immunology, Torrey Pines Institute for Molecular Studies, San Diego, California, USA
BMC Bioinformatics 2009, 10:394 doi:10.1186/1471-2105-10-394
Published: 30 November 2009Additional files
Additional file 1:
Raw binding affinity data of combinatorial peptide scanning library against the 24 MHC molecules. Binding affinity measurements of each peptide library are shown for all 24 MHC molecules. Each row represents a peptide library, which corresponds to a fixed residue at a given position. Columns span the 24 MHC molecules.
Format: TXT Size: 55KB Download file
Additional file 2:
Peptide:MHC Binding Energy Covariance Matrix. This covariance matrix was calculated from the raw binding in Dataset S1. The symmetric matrix has dimensions of 20 × 20. Each entry represents how two residues contribute to binding affinities with respect to each other. A positive value indicates they are alike; a negative value indicates they are different.
Format: MAT Size: 7KB Download file
Additional file 3:
Prediction performances of NetMHC, SMM, SMMPMBEC, and SMMBLOSUM. This is an expanded version of benchmark results shown in the manuscript by including prediction performances of SMMBLOSUM.
Format: XLS Size: 14KB Download file
This file can be viewed with: Microsoft Excel Viewer