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A comparative in silico linear B-cell epitope prediction and characterization for South American and African Trypanosoma vivax strains

Rafael Lucas Muniz Guedes, Carla Monadeli Filgueira Rodrigues, Nicolas Coatnoan, Alain Cosson, Fabiano Antonio Cadioli, Herakles Antonio Garcia, Alexandra Lehmkuhl Gerber, Rosangela Zacarias Machado, Paola Marcella Camargo Minoprio, Marta Maria Geraldes Teixeira, Ana Tereza Ribeiro de Vasconcelos
2018 Genomics  
to identify and characterize putative linear B-cell epitopes from African and South American T. vivax.  ...  transcriptome of a virulent T. vivax strain (Lins), isolated from an outbreak of severe disease in South America (Brazil) and performed a computational integrated analysis of genome, transcriptome and in silico predictions  ...  The authors are indebted to the MAEDI, Chaire USP/ Pasteur, RLMG and CMR received three months Calmette & Yersin fellowships from the Institut Pasteur International Division.  ... 
doi:10.1016/j.ygeno.2018.02.017 pmid:29499243 fatcat:dzyy7tu7rbh2tcgvkhnwxyrgau

Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins

Johannes Sollner, Rainer Grohmann, Ronald Rapberger, Paul Perco, Arno Lukas, Bernd Mayer
2008 Immunome Research  
We have investigated the integration of B-cell epitope prediction with the variability of antigen and the conservation of patterns for post-translational modification (PTM) prediction to improve over state  ...  Based on this dataset machine-learning methods further improve predictive power to a class separation in an equilibrated dataset of up to 83%.  ...  Protectivity Analysis and Prediction Effect of domain-accessibility filtering on protectivity prediction To assess the effect of domain accessibility filtering (masking) from protectivity prediction  ... 
doi:10.1186/1745-7580-4-1 pmid:18179690 pmcid:PMC2244602 fatcat:svhukirqcbhtdfls5gevwdum24

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

Pingping Sun, Haixu Ju, Zhenbang Liu, Qiao Ning, Jian Zhang, Xiaowei Zhao, Yanxin Huang, Zhiqiang Ma, Yuxin Li
2013 Computational and Mathematical Methods in Medicine  
Localizing epitopes by experimental methods is expensive in terms of time, cost, and effort; therefore, computational methods feature for its low cost and high speed was employed to predict B-cell epitopes  ...  In this paper, we review the recent advance of bioinformatics resources and tools in conformational B-cell epitope prediction, including databases, algorithms, web servers, and their applications in solving  ...  It aligns each mimotope to the antigen sequence and then selects the most mutually compatible alignments from a set of the top-scoring alignments before filtering out spurious alignments with EPIFILTER  ... 
doi:10.1155/2013/943636 pmid:23970944 pmcid:PMC3736542 fatcat:52htw2wq2fcg3bnl6f5zndxpde

Bioinformatics Resources and Tools for Phage Display

Jian Huang, Beibei Ru, Ping Dai
2011 Molecules  
With the improvement of these tools, they are expected to serve the phage display community better.  ...  Although these bioinformatics resources have been widely used to exclude target-unrelated peptides, characterize small molecules-protein interactions and map protein-protein interactions, a lot of problems  ...  Acknowledgements The authors are grateful to the anonymous reviewers for their valuable comments, which have led to the improvement of this review.  ... 
doi:10.3390/molecules16010694 pmid:21245805 pmcid:PMC6259106 fatcat:gvc7a3dtfreinjyakmcyt56kbm

Landscape and Selection of Vaccine Epitopes in SARS-CoV-2 [article]

Christof C Smith, Sarah Entwistle, Caryn Willis, Steven Vensko, Wolfgang Beck, Jason Garness, Maria Sambade, Eric Routh, Kelly Olsen, Julia Kodysh, Timothy O'Donnell, Carsten Haber (+8 others)
2020 biorxiv/medrxiv  
B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering to select regions with surface accessibility, high sequence conservation, spatial  ...  In this study, we combine computational prediction of T cell epitopes, recently published B cell epitope mapping studies, and epitope accessibility to select candidate peptide vaccines for SARS-CoV-2.  ...  We would like to thank members of the #DownWithTheCrown Slack channel for helpful discussion and feedback.  ... 
doi:10.1101/2020.06.04.135004 pmid:32577654 pmcid:PMC7302209 fatcat:uzuqf6onbrdlxpkf5btlin23km

Landscape and selection of vaccine epitopes in SARS-CoV-2

Christof C. Smith, Kelly S. Olsen, Kaylee M. Gentry, Maria Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter (+16 others)
2021 Genome Medicine  
B cell epitope regions were chosen from linear epitope mapping studies of convalescent patient serum, followed by filtering for surface accessibility, sequence conservation, spatial localization near functional  ...  Further studies are needed to optimize prediction and induction of B cell responses, as well as study the protective capacity of predicted T and B cell epitopes.  ...  Acknowledgements We would like to thank members of the #DownWithTheCrown Slack channel for helpful discussion and feedback.  ... 
doi:10.1186/s13073-021-00910-1 pmid:34127050 pmcid:PMC8201469 fatcat:epiym7kcsbfgzhn2jb3porytla

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm

Itay Mayrose, Tomer Shlomi, Nimrod D. Rubinstein, Jonathan M. Gershoni, Eytan Ruppin, Roded Sharan, Tal Pupko
2006 Nucleic Acids Research  
The problem of epitope mapping is converted into the task of aligning a set of query peptides to a graph representing the surface of the antigen.  ...  We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs.  ...  Funding to pay the Open Access publication charges for this article was provided by a research grant from the Ministry of Science and Technology, Israel to T.P. Conflict of interest statement.  ... 
doi:10.1093/nar/gkl975 pmid:17151070 pmcid:PMC1761437 fatcat:kgwoi4irereizntfv33stulffe

SPADE web service for prediction of allergen IgE epitopes

2019 Nucleic Acids Research  
Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes.  ...  Only few allergen-specific IgE epitopes have been determined experimentally to date.  ...  Specifically, it will be interesting to see, whether the inclusion of a proven non-cross-reactive protein in the analysis can improve the specificity of the prediction.  ... 
doi:10.1093/nar/gkz331 pmid:31066444 pmcid:PMC6602491 fatcat:hljntujejzaytbuqljf6eazt2m

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

Julia V Ponomarenko, Philip E Bourne
2007 BMC Structural Biology  
Conclusion: It may be possible to improve epitope prediction methods through training on datasets which include only immune epitopes and through utilizing more features characterizing epitopes, for example  ...  The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics.  ...  The authors would like to acknowledge Dr. Alex Sette and Dr. Bjoern Peters from the La Jolla Institute of Allergy and Immunology (LIAI) and Dr.  ... 
doi:10.1186/1472-6807-7-64 pmid:17910770 pmcid:PMC2174481 fatcat:bv3iztfac5fozdwakibduihcdm

In silico Homology Modeling and Epitope Prediction of NadA as a Potential Vaccine Candidate in Neisseria meningitidis

Narjes Shahsavani, Mohammad Hasan Sheikhha, Hassan Yousefi, Fatemeh Sefid
2018 International journal of molecular and cellular medicine  
Locations of important linear and conformational epitopes were determined and conserved residues were identified to broaden our knowledge of efficient vaccine design to reduce meningococcal infectioun  ...  In the present study, we exploited bioinformatics tools to better understand and determine the 3D structure of NadA and its functional residues to select B cell epitopes, and provide information for elucidating  ...  EPCES at was used to predictp antigenic epitopes on protein surfaces.  ... 
doi:10.22088/ijmcm.bums.7.1.53 pmid:30234073 pmcid:PMC6134420 fatcat:y4hyfnky55gbladep7wozirt2q

Prediction and evolution of B cell epitopes of surface protein in SARS-CoV-2

Jerome Rumdon Lon, Yunmeng Bai, Bingxu Zhong, Fuqiang Cai, Hongli Du
2020 Virology Journal  
Based on the NCBI Reference Sequence: NC_045512.2, the conformational and linear B cell epitopes of the surface protein were predicted separately by various prediction methods.  ...  Background In order to obtain antibodies that recognize natural proteins, it is possible to predict the antigenic determinants of natural proteins, which are eventually embodied as polypeptides.  ...  Prediction of linear B cell epitopes All linear B cell epitopes of the surface protein were filtered according to the following criteria: (1) region with high surface probability (≥ 0.75), strong antigenicity  ... 
doi:10.1186/s12985-020-01437-4 pmid:33121513 fatcat:h24zti25kbhzlg73hi3d6put5u

Recent advances in B-cell epitope prediction methods

Yasser EL-Manzalawy, Vasant Honavar
2010 Immunome Research  
We review recent advances in computational methods for B-cell epitope prediction, identify some gaps in the current state of the art, and outline some promising directions for improving the reliability  ...  Although several computational tools for predicting B-cell epitopes have become available in recent years, the predictive performance of existing tools remains far from ideal.  ...  Acknowledgements This research was supported in part by a grant from the National Institutes of Health (GM066387) to Vasant Honavar.  ... 
doi:10.1186/1745-7580-6-s2-s2 pmid:21067544 pmcid:PMC2981878 fatcat:3zjfvl2fkjgxdakyxrah2ioioa

Biochemical characterization of PE_PGRS61 family protein of Mycobacterium tuberculosis H37Rv reveals the binding ability to fibronectin

Monu, Laxman S Meena
2016 Iranian Journal of Basic Medical Sciences  
Moreover, for better understanding the computational analysis, the B-cell and T-cell epitopes prediction prospect some amino acid propensity scales with hydrophilicity and antigenic variation index at  ...  Thus, the current findings provide an opportunity to illuminate the functions of PE_PGRS61 family protein.  ...  B-cell and T-cell epitopes prediction The PE_PGRS61 protein primary sequence was used to predict B-cell and T-cell epitopes with various online bioinformatics tools.  ... 
pmid:27872707 pmcid:PMC5110659 fatcat:3mdebyh6wfgnxd6qv7frmy7chu

Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding

Linling He, Yushao Cheng, Leopold Kong, Parisa Azadnia, Erick Giang, Justin Kim, Malcolm R. Wood, Ian A. Wilson, Mansun Law, Jiang Zhu
2015 Scientific Reports  
Scaffolding, by grafting an epitope onto a heterologous protein scaffold, offers a possible solution to epitope vaccine design.  ...  We first combined six structural alignment algorithms in a "scaffolding meta-server" to search for diverse scaffolds that can structurally accommodate the HCV epitopes.  ...  prediction problems 48 , we sought to develop a scaffolding meta-server to facilitate epitope vaccine design.  ... 
doi:10.1038/srep12501 pmid:26238798 pmcid:PMC4533164 fatcat:qizhz35msnfyljnyadywb4lz6u

Epitope‐based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study

Muhammad Tahir ul Qamar, Saman Saleem, Usman Ali Ashfaq, Amna Bari, Farooq Anwar, Safar Alqahtani
2019 Journal of Translational Medicine  
This infectious single-stranded, positive (+) sense RNA virus enters the host by binding to dipeptidyl-peptide receptors.  ...  Since no vaccine is yet available for MERS-COV, rapid case identification, isolation, and infection prevention strategies must be used to combat the spreading of MERS-COV infection.  ...  Acknowledgements Authors would like to acknowledge Huazhong Agricultural University, Wuhan, China and Prince Sattam bin Abdul Aziz University, Alkharj, Saudi Arabia for providing facilities for this study  ... 
doi:10.1186/s12967-019-2116-8 pmid:31703698 pmcid:PMC6839065 fatcat:cm4oybog2ffl5hveehqyshyrzu
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