How to cite


When using this WebApp, please always cite MHCcombine AND the prediction algorithm that was queried to retrieve your results. For your convenience, a list of the respective references is given below.

To cite MHCcombine please refer to:

M. Bonsack, S. Hoppe, J. Winter, C. Zeller, M. D. Küpper, E. Schitter, R. Blatnik, A. B. Riemer

Performance evaluation of MHC class-I binding prediction tools based on an experimentally validated MHC-peptide binding dataset.

submitted


To cite the respective prediction servers and algorithms please refer to:

NetMHCpan 4.0

V. Jurtz, S. Paul, M. Andreatta,P. Marcatili, B. Peters, M. Nielsen

NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.

The Journal of Immunology (2017) PMID: 28978689


M. Andreatta, M. Nielsen

NetMHCpan-3.0: improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets.

Genome Medicine (2016) PMID: 27029192


I. Hoof, B. Peters, J. Sidney, L. E. Pedersen, A. Sette, O. Lund, S. Buus, and M. Nielsen

NetMHCpan, a method for MHC class I binding prediction beyond humans.

Immunogenetics (2009) PMID: 19002680


NetMHC 4.0

M. Andreatta, M. Nielsen

Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

Bioinformatics (2016) PMID: 26515819


M. Nielsen, C. Lundegaard, P. Worning, S. L. Lauemøller, K. Lamberth, S. Buus, S. Brunak, and O. Lund

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.

Protein Science (2003) PMID: 12717023


NetMHC 3.4

M. Nielsen, C. Lundegaard, P. Worning, S. L. Lauemøller, K. Lamberth, S. Buus, S. Brunak, and O. Lund

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations.

Protein Science (2003) PMID: 12717023


C. Lundegaard, K. Lamberth, M. Harndahl, S. Buus, O. Lund, and M. Nielsen

NetMHC-3.0: Accurate web accessible predictions of Human, Mouse, and Monkey MHC class I affinities for peptides of length 8-11.

Nucleic Acids Research - Web Server Issue (2008) PMID: 18463140


If peptide lengths other than 9mers were predicted please cite:

C. Lundegaard, O. Lund, and M. Nielsen

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers.

Bioinformatics (2008) PMID: 18413329


NetMHCpan 3.0

M. Andreatta, M. Nielsen

NetMHCpan-3.0: improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets.

Genome Medicine (2016) PMID: 27029192


I. Hoof, B. Peters, J. Sidney, L. E. Pedersen, A. Sette, O. Lund, S. Buus, and M. Nielsen

NetMHCpan, a method for MHC class I binding prediction beyond humans.

Immunogenetics (2009) PMID: 19002680


NetMHCpan 2.8

I. Hoof, Peters B, J. Sidney, L. Pedersen, A. Sette, O. Lund, S. Buus, M. Nielsen

NetMHCpan, a method for MHC class I binding prediction beyond humans.

Immunogenetics (2007) PMID: 19002680


M. Nielsen, C. Lundegaard, T. Blicher, K. Lamberth, M. Harndahl, S. Justesen, G. Roder, B. Peters, A. Sette, O. Lund, S. Buus

NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.

PLoS One (2007) PMID: 17726526


NetMHCcons 1.1

E. Karosiene, C. Lundegaard, O. Lund, M. Nielsen

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions.

Immunogenetics (2012) PMID: 22009319


PickPocket 1.1

H. Zhang, O. Lund, M. Nielsen

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding .

Bioinformatics (2009) PMID: 19297351


IEDB Consensus

M. Moutaftsi, B. Peters, V. Pasquetto, D. Tscharke, J. Sidney, H. Bui, H. Grey, A. Sette

A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus.

Nature Biotechnology (2006) PMID: 16767078


IEDB SMMPMBEC

Y. Kim, J. Sidney, C. Pinilla, A. Sette, B. Peters

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior.

BMC Bioinformatics (2009) PMID: 19948066


IEDB SMM

B. Peters, A. Sette

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.

BMC Bioinformatics (2005) PMID: 15927070


SYFPEITHI

H. Rammensee, J. Bachmann, N. N. Emmerich, O. A. Bachor and S. Stevanovic

SYFPEITHI: database for MHC ligands and peptide motifs.

Immunogenetics (1999) PMID: 10602881



References about HLA supertypes

A. Sette, and J. Sidney

Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism.

Immunogenetics (1999) PMID: 10602880


O. Lund, M. Nielsen, C. Kesmir, A. G. Petersen, C. Lundegaard, P. Worning, C. Sylvester-Hvid, K. Lamberth, G. Roder, S. Justesen, S. Buus, and S. Brunak

Definition of supertypes for HLA molecules using clustering of specificity matrices.

Immunogenetics (2004) PMID: 14963618


J. Sidney, B. Peters, N. Frahm, C. Brander, and A. Sette

HLA class I supertypes: a revised and updated classification.

BMC Immunology (2008) PMID: 18211710