Software for designing epitope based vaccine

jQuery UI Tabs - Default functionality The page provides list of software realted to immunoinformatics or vaccine informatics. These packages are important for researcher working in the field of epitope or peptide based vaccines. In OSDDlinux we have divided in categories i) All for all type ofsoftware, ii) Webservers for web services, iii) Galaxy for software integated in Galaxy, iv) GUI for graphics based software, v) Third for software not belongs to Raghava's group

Software nameDescription
PROPRED1 The ProPred-I software is useful for identification of MHC Class-I binding regions in antigens.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
Pcleavage A SVM based method for prediction of protesosomal cleavage site in a protein sequence.
TPPred TAPPred is an on-line service for predicting binding affinity of peptides toward the TAP transporter.
CTLPred CTLPred is a direct method for prediction of CTL epitopes crucial in subunit vaccine design.
ProPred The aim of this server is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices.
HLA-DR4Pred The HLA-DR4Pred is an SVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction method.
MHC In this prediction method we have used Matrix Optimization Technique to predict MHC binding core.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
ABCPred The aim of ABCpred server is to predict B cell epitope(s) in an antigen sequence, using artificial neural network.
CBTOPE Conformational B cell prediction method: In the present study using amino acid composition as an input feature for Support vector machine (SVM).
LBTOPE Predict of B-cell epitopes (antigenic region) with high accuracy is one of the major challenges in designing subunit/peptide vaccine or immunotherapy.

Software nameDescription
PROPRED1 The ProPred-I software is useful for identification of MHC Class-I binding regions in antigens.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
Pcleavage A SVM based method for prediction of protesosomal cleavage site in a protein sequence.
TPPred TAPPred is an on-line service for predicting binding affinity of peptides toward the TAP transporter.
CTLPred CTLPred is a direct method for prediction of CTL epitopes crucial in subunit vaccine design.
ProPred The aim of this server is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices.
HLA-DR4Pred The HLA-DR4Pred is an SVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction method.
MHC In this prediction method we have used Matrix Optimization Technique to predict MHC binding core.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
ABCPred The aim of ABCpred server is to predict B cell epitope(s) in an antigen sequence, using artificial neural network.
CBTOPE Conformational B cell prediction method: In the present study using amino acid composition as an input feature for Support vector machine (SVM).
LBTOPE Predict of B-cell epitopes (antigenic region) with high accuracy is one of the major challenges in designing subunit/peptide vaccine or immunotherapy.

Software nameUsage
PROPRED1 propred1.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put folder
nHLApred nhla4pred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
Pcleavage pcleavage.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
TAPPred tabpred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
CTLPred ctlpred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
ProPred propred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
HLA-DR4 Pred hladr4pred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
MHC mhc.pl -i input_file -a allele -o output -i Sequence in FASTA format -a: Select Allele: 1 for HLA-DR1, 2 for HLA-DR2, 3 for HLA-DR5 -o name of out put file
nHLApred nhla4pred.pl -i input_file -o output -p path -i Sequence in FASTA format -o name of out put file
ABCPred abcpred.pl -i input_file -t threshold -w window size -o output -i: input file in fasta format -t: Threshold Value (ranges from 0.1 to 1, Default is 0.5) -w: Window size (Default is 16) -o: output file
CBTOPE cbtope.pl -i input_file -o output -i: input file in fasta format -o: output file
LBTOPE cbtope.pl -i input_file -o output -i: input file in fasta format -o: output file

Software nameDescription
PROPRED1 The ProPred-I software is useful for identification of MHC Class-I binding regions in antigens.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
Pcleavage A SVM based method for prediction of protesosomal cleavage site in a protein sequence.
TPPred TAPPred is an on-line service for predicting binding affinity of peptides toward the TAP transporter.
CTLPred CTLPred is a direct method for prediction of CTL epitopes crucial in subunit vaccine design.
ProPred The aim of this server is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices.
HLA-DR4Pred The HLA-DR4Pred is an SVM and ANN based HLA-DRB1*0401(MHC class II alleles) binding peptides prediction method.
MHC In this prediction method we have used Matrix Optimization Technique to predict MHC binding core.
nHLApred This is a comprehensive method for prediction of MHC binding peptides or CTL epitopes of 67 MHC alleles.
ABCPred The aim of ABCpred server is to predict B cell epitope(s) in an antigen sequence, using artificial neural network.
CBTOPE Conformational B cell prediction method: In the present study using amino acid composition as an input feature for Support vector machine (SVM).
LBTOPE Predict of B-cell epitopes (antigenic region) with high accuracy is one of the major challenges in designing subunit/peptide vaccine or immunotherapy.

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