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Bioinformatics and Biology Insights

Synopsis: An open access, peer reviewed electronic journal that covers computational biology, particularly computational methods used in the analysis and annotation of structures.


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About this journal

ISSN: 1177-9322



Aims and scope:

Bioinformatics and Biology Insights is an open access, peer-reviewed journal that considers articles on computational methods used in the analysis and annotation of structures, in addition to other areas of computational biology and the broader field of biology.

It both complements Libertas Academica’s subject-specific journals in the area and also seeks to place bioinformatics in the broader context of biology. The journal welcomes all submissions in the field of bioinformatics and also submissions dealing with the relationship between bioinformatics and the broader field of biology. Submissions of original research, reviews, tutorials, rapid communications, expert commentaries, letters, application notes, and point–counter-point articles are welcomed for peer review. No word limits are imposed, but authors are reminded that excessive word-counts may attract adverse comment by peer reviewers and discourage readers.

The submission of tutorial-type articles is encouraged, in which methods which have been developed in the recent past are reviewed in such a way as to make them readily comprehensible for Biologists. Papers discussing methodologies are discouraged unless they explicitly demonstrate that new biological insights have been gained or that earlier methods used to gain a new insight can be replaced.

Authors are encouraged to consider submitting their manuscripts to Evolutionary Bioinformatics and Cancer Informatics, if they consider that their manuscript is exclusively or specifically relevant to those journals’ audiences.

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Submissions, excluding editorials, letters to the editor and dedications, will be peer reviewed by two reviewers.  Reviewers are required to provide fair, balanced and constructive reports.  

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Papers are not sent to peer reviewers following submission of a revised manuscript. Editorial decisions on re-submitted papers are based on the author's response to the initial peer review report.

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As of April 7 2008, the US NIH Public Access Policy requires that all peer reviewed articles resulting from research carried out with NIH funding be deposited in the Pubmed Central archive.

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Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences

Authors: Surendra S Negi and Werner Braun
Publication Date: 01 Jul 2009
Bioinformatics and Biology Insights 2009:3 71-81

Surendra S Negi and Werner Braun

Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, 77555-0857, USA.

Abstract

Background:  Precise determination of conformational epitopes of neutralizing antibodies represents a key step in the rational design of novel vaccines. A powerful experimental method to gain insights on the physical chemical nature of conformational epitopes is the selection of linear peptides that bind with high affinities to a monoclonal antibody of interest by phage display technology. However, the structural characterization of conformational epitopes from these mimotopes is not straightforward, and in the past the interpretation of peptide sequences from phage display experiments focused on linear sequence analysis to find a consensus sequence or common sequence motifs.

Results:  We present a fully automated search method, EpiSearch that predicts the possible location of conformational epitopes on the surface of an antigen. The algorithm uses peptide sequences from phage display experiments as input, and ranks all surface exposed patches according to the frequency distribution of similar residues in the peptides and in the patch. We have tested the performance of the EpiSearch algorithm for six experimental data sets of phage display experiments, the human epidermal growth factor receptor-2 (HER-2/neu), the antibody mAb Bo2C11 targeting the C2 domain of FVIII, antibodies mAb 17b and mAb b12 of the HIV envelope protein gp120, mAb 13b5 targeting HIV-1 capsid protein and 80R of the SARS coronavirus spike protein. In all these examples the conformational epitopes as determined by the X-ray crystal structures of the antibody-antigen complexes, were found within the highest scoring patches of EpiSearch, covering in most cases more than 50% residues of experimental observed conformational epitopes. Input options of the program include mapping of a single peptide or a set of peptides on the antigen structure, and the results of the calculation can be visualized on our interactive web server.

Availability: Users can access the EpiSearch from our web server http://curie.utmb.edu/episearch.html

Categories: Bioinformatics


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