Literature DB >> 21331885

Advances of bioinformatics tools applied in virus epitopes prediction.

Ping Chen1, Simon Rayner, Kang-Hong Hu.   

Abstract

In recent years, the in silico epitopes prediction tools have facilitated the progress of vaccines development significantly and many have been applied to predict epitopes in viruses successfully. Herein, a general overview of different tools currently available, including T cell and B cell epitopes prediction tools, is presented. And the principles of different prediction algorithms are reviewed briefly. Finally, several examples are present to illustrate the application of the prediction tools.

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Year:  2011        PMID: 21331885      PMCID: PMC7090880          DOI: 10.1007/s12250-011-3159-4

Source DB:  PubMed          Journal:  Virol Sin        ISSN: 1995-820X            Impact factor:   4.327


  22 in total

Review 1.  SYFPEITHI: database for MHC ligands and peptide motifs.

Authors:  H Rammensee; J Bachmann; N P Emmerich; O A Bachor; S Stevanović
Journal:  Immunogenetics       Date:  1999-11       Impact factor: 2.846

2.  ProPred: prediction of HLA-DR binding sites.

Authors:  H Singh; G P Raghava
Journal:  Bioinformatics       Date:  2001-12       Impact factor: 6.937

3.  Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules.

Authors:  Hideki Noguchi; Ryuji Kato; Taizo Hanai; Yukari Matsubara; Hiroyuki Honda; Vladimir Brusic; Takeshi Kobayashi
Journal:  J Biosci Bioeng       Date:  2002       Impact factor: 2.894

4.  Prediction of residues in discontinuous B-cell epitopes using protein 3D structures.

Authors:  Pernille Haste Andersen; Morten Nielsen; Ole Lund
Journal:  Protein Sci       Date:  2006-09-25       Impact factor: 6.725

5.  Cytotoxic T-lymphocyte epitope vaccination protects against human metapneumovirus infection and disease in mice.

Authors:  Karen A Herd; Suresh Mahalingam; Ian M Mackay; Michael Nissen; Theo P Sloots; Robert W Tindle
Journal:  J Virol       Date:  2006-02       Impact factor: 5.103

Review 6.  Harnessing bioinformatics to discover new vaccines.

Authors:  Matthew N Davies; Darren R Flower
Journal:  Drug Discov Today       Date:  2007-04-06       Impact factor: 7.851

7.  Screening and identification of B cell epitopes of structural proteins of foot-and-mouth disease virus serotype Asia1.

Authors:  Zhong-Wang Zhang; Yong-Guang Zhang; Yong-Lu Wang; Li Pan; Yu-Zhen Fang; Shou-Tian Jiang; Jian-Liang Lü; Peng Zhou
Journal:  Vet Microbiol       Date:  2009-07-10       Impact factor: 3.293

8.  In silico prediction and ex vivo evaluation of potential T-cell epitopes in glycoproteins 4 and 5 and nucleocapsid protein of genotype-I (European) of porcine reproductive and respiratory syndrome virus.

Authors:  Ivan Díaz; Joan Pujols; Llilianne Ganges; Mariona Gimeno; Laila Darwich; Mariano Domingo; Enric Mateu
Journal:  Vaccine       Date:  2009-07-29       Impact factor: 3.641

9.  SVMHC: a server for prediction of MHC-binding peptides.

Authors:  Pierre Dönnes; Oliver Kohlbacher
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

10.  Prediction of MHC class I binding peptides, using SVMHC.

Authors:  Pierre Dönnes; Arne Elofsson
Journal:  BMC Bioinformatics       Date:  2002-09-11       Impact factor: 3.169

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  9 in total

1.  Design and Antigenic Epitopes Prediction of a New Trial Recombinant Multiepitopic Rotaviral Vaccine: In Silico Analyses.

Authors:  Sima Jafarpour; Hoda Ayat; Ali Mohammad Ahadi
Journal:  Viral Immunol       Date:  2015-05-12       Impact factor: 2.257

2.  Efficacy of co-immunization with the DNA and peptide vaccines containing SYCP1 and ACRBP epitopes in a murine triple-negative breast cancer model.

Authors:  Ashkan Safavi; Amirhosein Kefayat; Elham Mahdevar; Fatemeh Ghahremani; Navid Nezafat; Mohammad Hossein Modarressi
Journal:  Hum Vaccin Immunother       Date:  2020-06-04       Impact factor: 3.452

3.  Design and Construction of Chimeric VP8-S2 Antigen for Bovine Rotavirus and Bovine Coronavirus.

Authors:  Khadijeh Nasiri; Mohammadreza Nassiri; Mojtaba Tahmoorespur; Alireza Haghparast; Saeed Zibaee
Journal:  Adv Pharm Bull       Date:  2016-03-17

4.  BEST: improved prediction of B-cell epitopes from antigen sequences.

Authors:  Jianzhao Gao; Eshel Faraggi; Yaoqi Zhou; Jishou Ruan; Lukasz Kurgan
Journal:  PLoS One       Date:  2012-06-27       Impact factor: 3.240

5.  Inferring epitopes of a polymorphic antigen amidst broadly cross-reactive antibodies using protein microarrays: a study of OspC proteins of Borrelia burgdorferi.

Authors:  Elisabeth Baum; Arlo Z Randall; Michael Zeller; Alan G Barbour
Journal:  PLoS One       Date:  2013-06-24       Impact factor: 3.240

6.  Cloning, molecular analysis and epitopics prediction of a new chaperone GroEL Brucella melitensis antigen.

Authors:  Mohammad Hadi Sekhavati; Reza Majidzadeh Heravi; Mojtaba Tahmoorespur; Soheil Yousefi; Tooba Abbassi-Daloii; Rahebe Akbari
Journal:  Iran J Basic Med Sci       Date:  2015-05       Impact factor: 2.699

Review 7.  Predicting alloreactivity in transplantation.

Authors:  Kirsten Geneugelijk; Kirsten Anne Thus; Eric Spierings
Journal:  J Immunol Res       Date:  2014-04-28       Impact factor: 4.818

8.  Identification and evaluation of the novel immunodominant antigen Rv2351c from Mycobacterium tuberculosis.

Authors:  Xuezhi Wang; Shuangshuang Chen; Yongjuan Xu; Huajun Zheng; Tongyang Xiao; Yuqing Li; Xing Chen; Mingxiang Huang; Haifeng Zhang; Xijing Fang; Yi Jiang; Machao Li; Haican Liu; Kanglin Wan
Journal:  Emerg Microbes Infect       Date:  2017-06-07       Impact factor: 7.163

9.  Computational Design of Epitope-Enriched HIV-1 Gag Antigens with Preserved Structure and Function for Induction of Broad CD8+ T Cell Responses.

Authors:  Benedikt Asbach; Johannes P Meier; Matthias Pfeifer; Josef Köstler; Ralf Wagner
Journal:  Sci Rep       Date:  2018-07-26       Impact factor: 4.379

  9 in total

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