Cancer Immunity - Links to Web Tools

Updated: April 30, 2008

These links are provided for the convenience of World Wide Web users. Cancer Immunity is not responsible for the availability or content of these external sites, nor does Cancer Immunity endorse, warrant or guarantee the products, services, or information described or offered at these other Internet sites.

This selection of Web tools are freely available and allow users to analyse sequences on the Web. Commercial software or applications which must be downloaded and used locally have not been included. Links added in the last update are marked - NEW. To suggest additional links or if you discover that a link is broken, please contact the Editorial Office.

Proteasomal cleavage:

PAProC - Prediction Algorithm for Proteasomal Cleavages
Department of Immunology and Department of Biomathematics, Eberhard-Karls-University Tübingen - Tübingen, Germany
http://www.paproc.de/

NetChop - prediction of cleavage sites of the human proteasome
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetChop/

MAPPP - MHC-I Antigenic Peptide Processing Prediction (FragPredict)
Max Planck Institute for Infection Biology - Berlin, Germany
http://www.mpiib-berlin.mpg.de/MAPPP/

TAP binding:

TAPPred - prediction of TAP binding peptides
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/tappred/

MHC peptide binding:

RankPep - prediction of MHC binding peptides
Molecular Immunology Foundation
http://bio.dfci.harvard.edu/Tools/rankpep.html

MHCPred - prediction of binding affinities
Edward Jenner Institute for Vaccine Research - United Kingdom
http://www.jenner.ac.uk/MHCPred/

SYFPEITHI: Epitope prediction - prediction of binding affinities
Biomedical Informatics (BMI) - Heidelberg, Germany
http://www.syfpeithi.de/Scripts/MHCServer.dll/EpitopePrediction.htm

MHCBench - benchmark MHC binding peptide prediction algorithms
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/mhcbench/

HLA Peptide Binding Predictions (BIMAS) - prediction of binding affinities for HLA class I molecules
BioInformatics & Molecular Analysis Section, CBEL, CIT and NIH - Bethesda, MD
http://www-bimas.cit.nih.gov/molbio/hla_bind/

PREDEP - MHC Class I epitope prediction
Department of Molecular Genetics and Biotechnology, The Hebrew University of Jerusalem - Jerusalem, Israel
http://margalit.huji.ac.il/Teppred/mhc-bind/index.html

nHLAPred - MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/nhlapred/

ProPred-I - promiscuous MHC Class-I binding peptide prediction
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/propred1/

SVMHC - prediction of MHC class I binding peptides
Stockholm Bioinformatics Center, Stockholm University - Sweden
http://www-bs.informatik.uni-tuebingen.de/Services/SVMHC

EPIPREDICT - MHC class II binding peptide prediction
Institute of Immunology - Rikshospitalet, Oslo AND Dep. of Onkology/ Immunology, University Childrens Hospital - Tübingen, Germany
http://www.epipredict.de

ProPred - prediction of HLA-DR binding sites
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/propred/

NetMHC - prediction of binding affinities for HLA-A2 and H-2Kk
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHC/

NetMHCII - prediction of binding affinities for different HLA-DR
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHCII/

NetMHCpan - prediction of binding affinities for different HLA-A and -B
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetMHCpan/

MULTIPRED - prediction of promiscuous peptides that bind to multiple HLA alleles belonging to one HLA supertype
Institute for Infocomm Research - Singapore
http://antigen.i2r.a-star.edu.sg/multipred/

SMM - prediction of high affinity HLA-A2-binding peptides
Boston University - Boston, MA
http://zlab.bu.edu/SMM/

Antigenic peptides:

Prediction of Antigenic Determinants - prediction of peptides likely to elicit an antibody response
Molecular Immunology Foundation
http://bio.dfci.harvard.edu/Tools/antigenic.pl
Additional information: http://bio.dfci.harvard.edu/Tools/antigenic.html

ANTIGENIC (EMBOSS package) - prediction of peptides likely to elicit an antibody response
Swiss EMBnet Node - Switzerland
http://emboss.ch.embnet.org/Pise/antigenic.html

BepiPred - prediction of linear B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/BepiPred/

DiscoTope - prediction of discontinuous B-cell epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/DiscoTope/

CTL epitopes:

CTLPred - prediction of CTL epitopes
Bioinformatics Centre, Institute of Microbial Technology - Chandigarh, India
http://www.imtech.res.in/raghava/ctlpred/

EpiJen - prediction of T cell epitopes
Edward Jenner Institute for Vaccine Research - United Kingdom
http://www.jenner.ac.uk/EpiJen/

NetCTL - prediction of CTL epitopes
Center for Biological Sequence Analysis, Technical University of Denmark - Lyngby, Denmark
http://www.cbs.dtu.dk/services/NetCTL/

Tumor antigens:

VaxiJen - prediction of tumor antigens
Edward Jenner Institute for Vaccine Research - United Kingdom
http://www.jenner.ac.uk/VaxiJen/