SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity.

PubWeight™: 1.15‹?› | Rank: Top 10%

🔗 View Article (PMC 3440317)

Published in PLoS One on September 12, 2012

Authors

Bo Yao1, Lin Zhang, Shide Liang, Chi Zhang

Author Affiliations

1: School of Biological Sciences, Center for Plant Science and Innovation, University of Nebraska, Lincoln, Nebraska, United States of America.

Articles citing this

Prediction of IL4 inducing peptides. Clin Dev Immunol (2013) 0.92

A Novel Astrovirus-Like RNA Virus Detected in Human Stool. Virus Evol (2016) 0.91

Designing of interferon-gamma inducing MHC class-II binders. Biol Direct (2013) 0.86

Conformational B-cell epitopes prediction from sequences using cost-sensitive ensemble classifiers and spatial clustering. Biomed Res Int (2014) 0.85

Anopheles gambiae salivary protein expression modulated by wild Plasmodium falciparum infection: highlighting of new antigenic peptides as candidates of An. gambiae bites. Parasit Vectors (2014) 0.80

Tsetse GmmSRPN10 has anti-complement activity and is important for successful establishment of trypanosome infections in the fly midgut. PLoS Negl Trop Dis (2015) 0.79

Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni. BMC Res Notes (2014) 0.78

Prediction of linear B-cell epitopes of hepatitis C virus for vaccine development. BMC Med Genomics (2015) 0.78

EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression. BMC Bioinformatics (2014) 0.77

Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull. PLoS One (2015) 0.76

EBV-Associated Cancer and Autoimmunity: Searching for Therapies. Vaccines (Basel) (2015) 0.75

A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinformatics (2016) 0.75

Data on the epitope mapping of soybean A2 and A3 glycinin. Data Brief (2016) 0.75

An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. J Immunol Res (2016) 0.75

SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. BMC Bioinformatics (2017) 0.75

Antibodies to age-β2 glycoprotein I in patients with anti-phospholipid antibody syndrome. Clin Exp Immunol (2016) 0.75

Systematic Bioinformatic Approach for Prediction of Linear B-Cell Epitopes on Dengue E and prM Protein. Adv Bioinformatics (2016) 0.75

DRREP: deep ridge regressed epitope predictor. BMC Genomics (2017) 0.75

The Membrane-Proximal Region of C-C Chemokine Receptor Type 5 Participates in the Infection of HIV-1. Front Immunol (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics (1988) 70.41

Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A (1981) 32.98

NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res (2008) 26.04

Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry (1974) 12.07

The immune epitope database 2.0. Nucleic Acids Res (2009) 6.07

Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol (1985) 5.73

New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry (1986) 5.12

A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett (1990) 4.49

Improved method for predicting linear B-cell epitopes. Immunome Res (2006) 4.32

Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins (2006) 3.15

Predicting linear B-cell epitopes using string kernels. J Mol Recognit (2008) 2.47

Bcipep: a database of B-cell epitopes. BMC Genomics (2005) 2.27

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids (2007) 2.06

BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit (2003) 1.98

Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine (1999) 1.90

StAR: a simple tool for the statistical comparison of ROC curves. BMC Bioinformatics (2008) 1.85

Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett (1993) 1.65

The chemistry and mechanism of antibody binding to protein antigens. Adv Immunol (1988) 1.37

An SVM-based system for predicting protein subnuclear localizations. BMC Bioinformatics (2005) 1.24

Synthetic T and B cell recognition sites: implications for vaccine development. Adv Immunol (1989) 1.22

SVM-based prediction of linear B-cell epitopes using Bayes Feature Extraction. BMC Genomics (2010) 1.12

PREDITOP: a program for antigenicity prediction. J Mol Graph (1993) 1.10

FIMM, a database of functional molecular immunology. Nucleic Acids Res (2000) 1.06

BEST: improved prediction of B-cell epitopes from antigen sequences. PLoS One (2012) 0.99

Determinants of antigenicity and specificity in immune response for protein sequences. BMC Bioinformatics (2011) 0.94

Articles by these authors

Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survival. Nat Med (2004) 22.96

Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08

Genomewide association study of leprosy. N Engl J Med (2009) 8.17

The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat Cell Biol (2008) 7.86

A high-affinity conformation of Hsp90 confers tumour selectivity on Hsp90 inhibitors. Nature (2003) 7.69

Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A (2008) 6.59

Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet (2009) 6.42

Fragile X premutation tremor/ataxia syndrome: molecular, clinical, and neuroimaging correlates. Am J Hum Genet (2003) 5.51

Penetrance of the fragile X-associated tremor/ataxia syndrome in a premutation carrier population. JAMA (2004) 4.88

PUMA mediates the apoptotic response to p53 in colorectal cancer cells. Proc Natl Acad Sci U S A (2003) 4.46

Tumour hypoxia promotes tolerance and angiogenesis via CCL28 and T(reg) cells. Nature (2011) 4.07

miR-210 links hypoxia with cell cycle regulation and is deleted in human epithelial ovarian cancer. Cancer Biol Ther (2007) 3.93

Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One (2010) 3.64

Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. Nat Genet (2009) 3.59

Tumor-infiltrating dendritic cell precursors recruited by a beta-defensin contribute to vasculogenesis under the influence of Vegf-A. Nat Med (2004) 3.55

The TLR4 gene polymorphisms and susceptibility to cancer: a systematic review and meta-analysis. Eur J Cancer (2012) 3.41

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40

Distinct expression levels and patterns of stem cell marker, aldehyde dehydrogenase isoform 1 (ALDH1), in human epithelial cancers. PLoS One (2010) 3.38

Enhanced store overload-induced Ca2+ release and channel sensitivity to luminal Ca2+ activation are common defects of RyR2 mutations linked to ventricular tachycardia and sudden death. Circ Res (2005) 3.34

The Arabidopsis CORONATINE INSENSITIVE1 protein is a jasmonate receptor. Plant Cell (2009) 3.31

RyR2 mutations linked to ventricular tachycardia and sudden death reduce the threshold for store-overload-induced Ca2+ release (SOICR). Proc Natl Acad Sci U S A (2004) 3.25

Expanding window compressed sensing for non-uniform compressible signals. Sensors (Basel) (2012) 2.98

Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86

Early pottery at 20,000 years ago in Xianrendong Cave, China. Science (2012) 2.73

Fragile X-associated tremor/ataxia syndrome: clinical features, genetics, and testing guidelines. Mov Disord (2007) 2.68

PUMA regulates intestinal progenitor cell radiosensitivity and gastrointestinal syndrome. Cell Stem Cell (2008) 2.68

Enhanced basal activity of a cardiac Ca2+ release channel (ryanodine receptor) mutant associated with ventricular tachycardia and sudden death. Circ Res (2002) 2.64

Age-associated decrease in TLR function in primary human dendritic cells predicts influenza vaccine response. J Immunol (2010) 2.63

Metformin and prostate cancer: reduced development of castration-resistant disease and prostate cancer mortality. Eur Urol (2012) 2.45

Association analyses identify six new psoriasis susceptibility loci in the Chinese population. Nat Genet (2010) 2.41

MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer. Cancer Res (2008) 2.35

microRNA-21 negatively regulates Cdc25A and cell cycle progression in colon cancer cells. Cancer Res (2009) 2.32

Mechanisms of microRNA deregulation in human cancer. Cell Cycle (2008) 2.30

The transcriptional targets of p53 in apoptosis control. Biochem Biophys Res Commun (2005) 2.25

A homochiral porous metal-organic framework for highly enantioselective heterogeneous asymmetric catalysis. J Am Chem Soc (2005) 2.24

Generation of a triple-gene knockout mammalian cell line using engineered zinc-finger nucleases. Biotechnol Bioeng (2010) 2.23

Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19

ADAMTS-1 and ADAMTS-4 levels are elevated in thoracic aortic aneurysms and dissections. Ann Thorac Surg (2012) 2.18

Functional coupling of p38-induced up-regulation of BiP and activation of RNA-dependent protein kinase-like endoplasmic reticulum kinase to drug resistance of dormant carcinoma cells. Cancer Res (2006) 2.15

FSIM: a feature similarity index for image quality assessment. IEEE Trans Image Process (2011) 2.13

HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell (2005) 2.06

A novel 3D mammalian cell perfusion-culture system in microfluidic channels. Lab Chip (2007) 2.03

PUMA Dissociates Bax and Bcl-X(L) to induce apoptosis in colon cancer cells. J Biol Chem (2006) 2.02

Hedgehog signal transduction via Smoothened association with a cytoplasmic complex scaffolded by the atypical kinesin, Costal-2. Mol Cell (2003) 2.02

Following cytochrome c release, autophagy is inhibited during chemotherapy-induced apoptosis by caspase 8-mediated cleavage of Beclin 1. Cancer Res (2011) 1.99

Telephone-based re-education on the day before colonoscopy improves the quality of bowel preparation and the polyp detection rate: a prospective, colonoscopist-blinded, randomised, controlled study. Gut (2013) 1.97

KLF17 is a negative regulator of epithelial-mesenchymal transition and metastasis in breast cancer. Nat Cell Biol (2009) 1.97

Relationships of Indoor, Outdoor, and Personal Air (RIOPA). Part I. Collection methods and descriptive analyses. Res Rep Health Eff Inst (2005) 1.95

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. Nat Genet (2011) 1.95

Clinical regressions and broad immune activation following combination therapy targeting human NKT cells in myeloma. Blood (2012) 1.94

Carvedilol and its new analogs suppress arrhythmogenic store overload-induced Ca2+ release. Nat Med (2011) 1.88

Sulforaphane-induced G2/M phase cell cycle arrest involves checkpoint kinase 2-mediated phosphorylation of cell division cycle 25C. J Biol Chem (2004) 1.88

PUMA-mediated apoptosis drives chemical hepatocarcinogenesis in mice. Hepatology (2011) 1.82

Polysomnography performed in the unattended home versus the attended laboratory setting--Sleep Heart Health Study methodology. Sleep (2004) 1.81

Differential apoptotic response to the proteasome inhibitor Bortezomib [VELCADE, PS-341] in Bax-deficient and p21-deficient colon cancer cells. Cancer Biol Ther (2003) 1.80

catena-Poly[[tetra-kis(hexa-methyl-phos-pho-ramide-κO)bis-(nitrato-κO,O')neodymium(III)] [silver(I)-di-μ(2)-sulfido-tungsten(VI)-di-μ(2)-sulfido]]. Acta Crystallogr Sect E Struct Rep Online (2008) 1.78

Double-negative feedback loop between reprogramming factor LIN28 and microRNA let-7 regulates aldehyde dehydrogenase 1-positive cancer stem cells. Cancer Res (2010) 1.78

An integrative approach of linking traditional Chinese medicine pattern classification and biomedicine diagnosis. J Ethnopharmacol (2011) 1.77

Progression of tremor and ataxia in male carriers of the FMR1 premutation. Mov Disord (2007) 1.77

Novel method for high-throughput phenotyping of sleep in mice. Physiol Genomics (2006) 1.77

The nuclear function of p53 is required for PUMA-mediated apoptosis induced by DNA damage. Proc Natl Acad Sci U S A (2007) 1.73

catena-Poly[[tetra-kis(hexa-methyl-phospho-ramide-κO)bis-(nitrato-κO,O')lanthanum(III)] [silver(I)-di-μ(2)-sulfido-tungstate(VI)-di-μ(2)-sulfido]]. Acta Crystallogr Sect E Struct Rep Online (2008) 1.72

Selection against PUMA gene expression in Myc-driven B-cell lymphomagenesis. Mol Cell Biol (2008) 1.72

Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives. J Med Chem (2007) 1.70

HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J Exp Bot (2008) 1.69

EGFR-induced and PKCε monoubiquitylation-dependent NF-κB activation upregulates PKM2 expression and promotes tumorigenesis. Mol Cell (2012) 1.65

AKT2 confers protection against aortic aneurysms and dissections. Circ Res (2012) 1.65

FK-16 derived from the anticancer peptide LL-37 induces caspase-independent apoptosis and autophagic cell death in colon cancer cells. PLoS One (2013) 1.65

Glycaemia (haemoglobin A1c) and incident ischaemic stroke: the Atherosclerosis Risk in Communities (ARIC) Study. Lancet Neurol (2005) 1.64

Effect of calcium or vitamin D supplementation on vascular outcomes: a meta-analysis of randomized controlled trials. Int J Cardiol (2013) 1.63

Attenuation of tumor necrosis factor-alpha elevation and improved heart function by postconditioning for 60 seconds in patients with acute myocardial infarction. Chin Med J (Engl) (2010) 1.62

Syndrome differentiation in modern research of traditional Chinese medicine. J Ethnopharmacol (2012) 1.62

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins (2004) 1.60

PTEN regulates collagen-induced platelet activation. Blood (2010) 1.60

Reflection-mode submicron-resolution in vivo photoacoustic microscopy. J Biomed Opt (2012) 1.59

Evidence of selection for clones having genetic inactivation of the activin A type II receptor (ACVR2) gene in gastrointestinal cancers. Cancer Res (2003) 1.58

Treatment of fragile X-associated tremor ataxia syndrome (FXTAS) and related neurological problems. Clin Interv Aging (2008) 1.57

Neuropathic features in fragile X premutation carriers. Am J Med Genet A (2007) 1.56

p53 independent induction of PUMA mediates intestinal apoptosis in response to ischaemia-reperfusion. Gut (2006) 1.56

Translating the therapeutic potential of AZD4547 in FGFR1-amplified non-small cell lung cancer through the use of patient-derived tumor xenograft models. Clin Cancer Res (2012) 1.53

Protective effects of cathelicidin-encoding Lactococcus lactis in murine ulcerative colitis. J Gastroenterol Hepatol (2012) 1.53

No PUMA, no death: implications for p53-dependent apoptosis. Cancer Cell (2003) 1.52

Expression of hedgehog signaling molecules in lung cancer. Acta Histochem (2010) 1.52

FGFR2 gene amplification in gastric cancer predicts sensitivity to the selective FGFR inhibitor AZD4547. Clin Cancer Res (2013) 1.51

An important role for RUNX3 in human L1 transcription and retrotransposition. Nucleic Acids Res (2003) 1.51

Apparently low reproducibility of true differential expression discoveries in microarray studies. Bioinformatics (2008) 1.48

Phosphatidylinositol-3-kinase signaling mediates vascular smooth muscle cell expression of periostin in vivo and in vitro. Atherosclerosis (2005) 1.48

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci U S A (2013) 1.48

DNA methylation of human telomerase reverse transcriptase associated with leukocyte telomere length shortening in hyperhomocysteinemia-type hypertension in humans and in a rat model. Circ J (2014) 1.47

Free fatty acids inhibit insulin signaling-stimulated endothelial nitric oxide synthase activation through upregulating PTEN or inhibiting Akt kinase. Diabetes (2006) 1.46

catena-Poly[[tetra-kis-(hexa-methyl-phospho-ramide-κO)bis-(nitrato-κO,O')dysprosium(III)] [silver(I)-di-μ-sulfido-tungstate(VI)-di-μ-sulfido]]. Acta Crystallogr Sect E Struct Rep Online (2010) 1.46

Sp1 and p73 activate PUMA following serum starvation. Carcinogenesis (2008) 1.46

Different effects of ERβ and TROP2 expression in Chinese patients with early-stage colon cancer. Tumour Biol (2012) 1.46

Downregulation of Dkk3 activates beta-catenin/TCF-4 signaling in lung cancer. Carcinogenesis (2007) 1.46

The DIANA-mirExTra web server: from gene expression data to microRNA function. PLoS One (2010) 1.44

PUMA-mediated intestinal epithelial apoptosis contributes to ulcerative colitis in humans and mice. J Clin Invest (2011) 1.43

A novel model for evaluating the risk of hepatitis B recurrence after liver transplantation. Liver Int (2011) 1.43

PUMA sensitizes lung cancer cells to chemotherapeutic agents and irradiation. Clin Cancer Res (2006) 1.43