Reference on Databases and Prediction Algorithms for MHC I binding

Databases:

	SYFPEITHI - database of MHC ligands and peptide motifs.
	MHCPEP - a database of MHC binding peptides
	HIV Molecular Immunology Database MHCPEP HLA Ligand/Motif DATABASE MHCBN Datatabase: Comprehensive Database of MHC Binding and Non-binding Peptides HLA Ligand/Motif DATABASE JenPep Database: MHC and TAP ligands, plus T and B cell epitopes FIMM Database: T and B cell epitopes MPID: MHC-peptide interation Database

T cell epitopes and prediction

	EpiBase - Platform for HLA Class I/II epitope prediction and selection with a vaccine development (cancer and infectious diseases) and protein deimmunization focus (AlgoNomics NV, Belgium).
	EpiMatrix - T cell epitope prediction service; EpiVax, Inc.
	EPIPREDICT - Software for HLA class II epitope prediction.
	FIMM - integrated database of functional immunology, focusing on MHC, antigens, and diseases (Computational Immunology Group, Bioinformatics Centre (National University of Singapore)-Kent Ridge Digital Labs, Singapore (BIC-KRDL).
	HLA Ligand/Motif Database - Online facility from Univ. of Oklahoma Health Sciences Center (NIH funded).
	HLA peptide binding predictions Online facility from Bioinformatics & Molecular Analysis Section (BIMAS), NIH.
	IMGT - ImMunoGeneTics information system specialising in MHC, Ig and TcR molecules from all vertebrate species.
	JenPep (now AntiJen) - Online database of published, experimentally derived data for peptides binding to MHC class I, II and TAP molecules, and a separate T cell epitope database (Bioinformatics Group, The Edward Jenner Inst. for Vaccine Res., Compton, UK).
	MHCPred - quantitative prediction of peptide binding to major histocompatibility complexes (Bioinformatics Group, The Edward Jenner Inst. for Vaccine Res., Compton, UK).
	ProImmune - Company specialising in the synthesis of recombinant MHC-peptide complexes.
	ProPred - Online facility; MHC class II epitope prediction based on TEPITOPE virtual matrices (Bioinformatics Centre, Institute of Microbial Technology, India).
	ProPred I - Online facility; MHC class I binding peptide prediction (Bioinformatics Centre, Institute of Microbial Technology, India).
	SYFPEITHI - database of MHC ligands and peptide motifs.
	TEPITOPE - Virtual matrix-based epitope prediction software.

Proteasome Clevage TAP binding prediction    

	NetChop Proteasomal cleavages (MHC ligands) Artifical Neural Network
	PAProc  Prteasomal cleavage. Artifical Neural Network Kuttler, A.K. Nussbaum, T.P. Dick, H.-G. Rammensee, H. Schild, K.P. Hadeler, An algorithm for the prediction of proteasomal cleavages, J. Mol. Biol. 298 (2000), 417-429 , A.K. Nussbaum, C. Kuttler, K.P. Hadeler, H.-G. Rammensee, H. Schild, PAProC: A Prediction Algorithm for Proteasomal Cleavages available on the WWW, Immunogenetics 53 (2001), 87-94 For comprehensive background information, please refer to From the test tube to the World Wide Web - The cleavage specificity of the proteasome (A.K. Nussbaum, dissertation, University of Tuebingen, Germany, 2001).
	RANKPEP. Immunoproteasomal cleavage. N-gram statistics
	Epitope. Tap binding predictions

Meta Reources   

	Los Alamos
	MHCBN