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Protocols

ProPred specifications

Information


Unique identifier OMICS_20484
Name ProPred
Interface Web user interface
Restrictions to use None
Input data Sequences
Input format FASTA, PIR, EMBL
Output data Text, graphics
Output format GIF
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


Additional information


http://osddlinux.osdd.net/raghava/propred/page3.html

Publication for ProPred

ProPred citations

 (101)
call_split

The polymorphisms of LCR, E6, and E7 of HPV 58 isolates in Yunnan, Southwest China

2018
Virol J
PMCID: 5918753
PMID: 29695285
DOI: 10.1186/s12985-018-0986-7
call_split See protocol

[…] The ProPred-I server (http://www.imtech.res.in/raghava/propred1/) and ProPred server (http://www.imtech.res.in/raghava/propred/) were used to predict the major histocompatibility complex (MHC) class-I bin […]

library_books

Strategies to Improve the Clinical Utility of Saporin Based Targeted Toxins

2018
Toxins
PMCID: 5848183
PMID: 29438358
DOI: 10.3390/toxins10020082

[…] allelic variants of MHC class II. However, if the analysis is restricted to the most diffuse allelic forms of MHC class II (according to [,]) it can be observed that the computer analysis application PropRed [] shows for Sap-SO6 (), that there are a number of peptide sequences in the region 85–100 that are predicted to be recognized by the MHC class II alleles DRB_0401, DRB_0405, DRB_0802 and DRB_ […]

library_books

Prevention and Control Strategies to Counter Zika Virus, a Special Focus on Intervention Approaches against Vector Mosquitoes—Current Updates

2018
Front Microbiol
PMCID: 5809424
PMID: 29472902
DOI: 10.3389/fmicb.2018.00087

[…] eptor, which along with 9-amino acid long stretch of peptide/epitope forms a ligand for T-cell receptor (TCR). Such peptide sequences may be predicted using the different algorithms like TEPITOPE and ProPred. By this approach “promiscuous” CD4+ T-cell epitopes from the conserved E and M proteins of ZIKV can be predicted which are able to bind with multiple HLA-DR molecules, and hence could pave wa […]

library_books

Anti NF155 chronic inflammatory demyelinating polyradiculoneuropathy strongly associates to HLA DRB15

2017
PMCID: 5691853
PMID: 29145880
DOI: 10.1186/s12974-017-0996-1

[…] In silico assays to predict NF155 binding to specific DRB1 alleles were developed using the IEDB analysis resource consensus [, ] and ProPred [] tools during April and May 2017. The human NF155 sequence (NP_001153803.1) was used to predict peptides binding with higher affinity to those HLA alleles associated with anti-NF155+ antibod […]

call_split

Structure based antigenic epitope and PEGylation improve the efficacy of staphylokinase

2017
Microb Cell Fact
PMCID: 5686944
PMID: 29137636
DOI: 10.1186/s12934-017-0801-y
call_split See protocol

[…] was synthesized based on codon optimization. The optimized gene was subcloned into pET28a expression vector (Novagen, U.S.). According to active site (PDB code 2sak and 1bui) and epitope predication (ProPred-I, http://www.imtech.res.in/raghava/propred1/) [, ], five candidate PEGylation sites were selected and mutant to cysteine, including C79G, C82L, C84K, C97A, and C104R, respectively. The mutant […]

library_books

Genotype specific acquisition, evolution and adaptation of characteristic mutations in hepatitis E virus

2017
PMCID: 5955438
PMID: 28727933
DOI: 10.1080/21505594.2017.1358349

[…] une Epitope Database (IEDB). Similarly, 9-mer T cell epitopes (MHC class I and II), following the same criteria as B cell epitopes, were predicted by online T cell epitope prediction tools, including ProPred-I (MHCI) and ProPred (MHCII). ProPred-I and ProPred identify and predict 47 types of MHCI and 57 types of MHCII allele specific binding peptides in a provided protein, respectively. The predic […]

Citations

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ProPred institution(s)
Bioinformatics Centre, Institute of Microbial Technology, Sector 39A, Chandigarth, India
ProPred funding source(s)
Supported by Council if Scientific and Industrial Research (CSIR); Department of Biotechnology (DBT).

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