HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials

Mukherjee, Sumanta and Bhattacharyya, Chiranjib and Chandra, Nagasuma (2016) HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials. In: BIOINFORMATICS, 32 (15). pp. 2297-2305.

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Abstract

Motivation: T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics and are critically dependent on experimentally obtained training data. Analysis of a training set from Immune Epitope Database (IEDB) for several alleles indicates that the sampling of the peptide space is extremely sparse covering a tiny fraction of the possible non-amer space, and also heavily skewed, thus restricting the range of epitope prediction. Results: We present a new epitope prediction method that has four distinct computational modules: (i) structural modelling, estimating statistical pair-potentials and constraint derivation, (ii) implicit modelling and interaction profiling, (iii) feature representation and binding affinity prediction and (iv) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles. Conclusions: HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any Class-1 HLA allele, by estimating the binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It relies on the strength of the mechanistic understanding of peptide-HLA recognition and provides an estimate of the total ligand space for each allele. The performance of HLaffy is seen to be superior to the currently available methods. Availability and implementation: The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy.

Item Type:	Journal Article
Publication:	BIOINFORMATICS
Additional Information:	Copy right for this article belongs to the OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
Department/Centre:	Division of Biological Sciences > Biochemistry Division of Electrical Sciences > Computer Science & Automation Division of Physical & Mathematical Sciences > Mathematics
Date Deposited:	22 Oct 2016 10:16
Last Modified:	22 Oct 2016 10:16
URI:	http://eprints.iisc.ac.in/id/eprint/55096

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