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Protocols

SVMHC specifications

Information


Unique identifier OMICS_06764
Name SVMHC
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Publication for SVMHC

SVMHC citations

 (17)
library_books

Bioinformatic prediction of the epitopes of Echinococcus granulosus antigen 5

2016
PMCID: 5351307
PMID: 28357070
DOI: 10.3892/br.2016.827

[…] LA-A*1101 and HLA-A*2401 cytotoxic T lymphocyte restricted epitopes of platelet membrane glycoprotein IIb/IIIa (GP IIb/IIIa) antibody of human and mice were predicted using SYFPEITHI, RANKPEP, BIMAS, SVMHC, PREDEP, MHCPRED and PROPRED software, and the T cell epitopes of GP IIb/IIIa antibody were predicted. In a different study conducted by Shen et al (), the secondary structure and surface charac […]

library_books

Immunoinformatics and epitope prediction in the age of genomic medicine

2015
Genome Med
PMCID: 4654883
PMID: 26589500
DOI: 10.1186/s13073-015-0245-0

[…] predictors need to be trained on large amounts of experimental data. Among the most popular methods are PSSM-based predictors (e.g., SYFPEITHI [], RANKPEP [] or BIMAS []), SVM-based predictors {e.g., SVMHC [], SVRMHC []) and ANN-based methods (e.g., netMHC [])}. To find the most accurate prediction tool, several benchmarks have been performed [–], but their results differ greatly, primarily owing […]

library_books

Sequence conservation analysis and in silico human leukocyte antigen peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens

2015
BMC Immunol
PMCID: 4619029
PMID: 26493839
DOI: 10.1186/s12865-015-0119-7

[…] MHC-I-binding predictions for the A*02:01, A*03:01 and B*07:02 alleles were done for 9-mer peptides in Mtb72F using NetCTLpan-1 [], NetMHCpan-2.2 [], SVMHC, Syfpeithi [], EpiJen [], nHLA-pred (nHLA-compred and nHLA-aanpred) and NetCTL-1.2 []. Results are presented as the individual outputs of NetCTLpan-1 and NetMHCpan-2.2 (which have been reported […]

library_books

Machine Learning Methods for Predicting HLA–Peptide Binding Activity

2015
Bioinform Biol Insights
PMCID: 4603527
PMID: 26512199
DOI: 10.4137/BBI.S29466

[…] Sparse encoding is simple but widely used by servers such as ANNPred/nHLAPred, MHC2PRED, NetMHC/NetMHCII,, NetMHC-pan/NetMHCIIpan,, SVMHC,, and SVRMHC. The concept of sparse encoding is similar to dummy variables in the machine learning field. Since each position within a sequence can be any of 20 different amino acids, a position […]

call_split

Identification of human leukemia antigen A*0201 restricted epitopes derived from epidermal growth factor pathway substrate number 8

2015
PMCID: 4463842
PMID: 25936538
DOI: 10.3892/mmr.2015.3673
call_split See protocol

[…] Third, protein sequences were analyzed with five different algorithms for HLA-A*0201, including immune epitope database (IEDB; http://www.iedb.org/), NetMHC (http://www.cbs.dtu.dk/services/NetMHC/), SVMHC (http://www.sbc.su.se/~pierre/svmhc/), EpiJen (http://www.ddgpharmfac.net/epijen/EpiJen/EpiJen.htm) and Rankpep (http://imed.med.ucm.es/Tools/rankpep.html). Peptides predicted by at least four a […]

call_split

Prediction of CD8+ Epitopes in Leishmania braziliensis Proteins Using EPIBOT: In Silico Search and In Vivo Validation

2015
PLoS One
PMCID: 4407964
PMID: 25905908
DOI: 10.1371/journal.pone.0124786
call_split See protocol

[…] EPIBOT callibration and training. To measure the accuracy of the prediction tools (netMHC, SYFPEITHII, BIMAS, SVMHC and IEDB), we initially provided EPIBOT with a dataset of proteins containing known CD8+ epitopes: we used a set of 4251 H2-Kd epitopes, available in IEDB. However, among these only 831 proteins […]

Citations

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SVMHC institution(s)
Division for Simulation of Biological Systems, WSI/ZBIT, Eberhard Karls University,Tübingen, Germany

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