scholarly journals PEPOP: new approaches to mimic non-continous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre de Brevern ◽  
Liza Felicori ◽  
Christophe NGuyen ◽  
Ricardo Andrez Machado de Avila ◽  
...  
Keyword(s):  
Binding Sites ◽  
Web Site ◽  
Peptide Design ◽  
Antigenic Peptides ◽  
New Methods ◽  
Bioinformatics Tools ◽  
Peptide Prediction ◽  
User Friendly ◽  
Discontinuous Epitopes ◽  
Cognate Protein

AbstractBioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits as replacing a protein difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitope predicted by bioinformatics tools are commonly used and these sequential epitopes are used as such in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools proposed so far to predict peptide sequences: Superficial and PEPOP. PEPOP can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. We have developed an improved version of PEPOP dedicated to answer to the experimentalists’ need for a tool able to handle proteins and to turn them into peptides. The PEPOP web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature.We present the user-friendly, well-structured web-site of PEPOP and its validation through the use of predicted immunogenic or antigenic peptides mimicking discontinuous epitopes in different experimental ways. PEPOP proposes 35 methods of peptide design to guide experimentalists in using peptides potentially capable of replacing the cognate protein in its interaction with an Ab.

scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Discontinuous Epitopes ◽  
Cognate Protein ◽  
Better Than

Abstract Background Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances. Results Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method. Conclusion The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

scholarly journals Benchmarking the PEPOP methods for mimicking discontinuous epitopes

2018 ◽  
Author(s):  
Vincent Demolombe ◽  
Alexandre G. de Brevern ◽  
Franck Molina ◽  
Géraldine Lavigne ◽  
Claude Granier ◽  
...  
Keyword(s):  
Protein Antigens ◽  
X Ray Crystallography ◽  
New Methods ◽  
Comparable Method ◽  
Version 2.0 ◽  
Peptide Prediction ◽  
The Traveling Salesman Problem ◽  
Antigen Antibody ◽  
Discontinuous Epitopes ◽  
Better Than

AbstractComputational methods provide approaches to identify epitopes in protein antigens to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein antigen in its interaction with an antibody. In the present work, we describe these new methods and the benchmarking of their performances.Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 antigen-antibody complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method.The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.

Component Based Method for Usability Testing of a Website

2013 ◽  
Vol 765-767 ◽  
pp. 1507-1511
Author(s):  
Saeeda Sharmeen Rahman ◽  
Jing Nong Weng
Keyword(s):  
Software Engineering ◽  
Modular Forms ◽  
Web Site ◽  
Usability Testing ◽  
Test Results ◽  
Testing Method ◽  
Component Based Software Engineering ◽  
User Friendly ◽  
University Web Site ◽  
The Web

This paper presents the Component-Based Software Engineering (CBSE) approach for usability testing of a web-site based on ISO 9241-11 usability guidance to achieve specified goals with effectiveness, efficiency and satisfaction. Usability testing is a technique used to evaluate a product by testing it on users. A particular type of website i.e. university web site was chosen and segmented in different components in modular forms according to the purpose of that component. Then component wise tasks as per ISO 9241-11 usability guidance were prepared to carry out the usability testing for evaluating the test web-site. After analyzing the results of component based usability testing, a proto-type version of the test web-site was designed in a limited form including all the feedback of test results. Finally, the proto-type web-site was re-evaluated for establishing the effectiveness of component based web usability method with the same tasks. The proposed component based usability testing method is expected to improve the design/content issues of web-site resulting the web-site much more user friendly, effective and less time and cost consuming.

Web Site Mobilization Techniques

2019 ◽  
pp. 1837-1845
Author(s):  
John Christopher Sandvig
Keyword(s):  
Mobile Devices ◽  
Web Sites ◽  
Web Site ◽  
Web Design ◽  
Laptop Computers ◽  
Digital Devices ◽  
Advantages And Disadvantages ◽  
Desktop Computers ◽  
Physical Limitations ◽  
User Friendly

Mobile-friendly websites are designed to render well on all digital devices, including smartphones, desktop computers, laptop computers, and tablets. Creating a user-friendly experience on mobile devices requires specific web design techniques. These techniques are designed to accommodate the small screens and other physical limitations of mobile devices. This chapter describes the three primary techniques for creating mobile-friendly web sites: responsive, separate URL, and server adaptive. It explains how each technique is implemented, the advantages and disadvantages of each, and their relative popularity. It also describes an emerging mobile technique called accelerated mobile pages.

The Web Site and Brand Trust as Antecedents of Online Loyalty

2011 ◽  
Vol 1 (2) ◽  
pp. 24-42 ◽  
Author(s):  
Horst Treiblmaier ◽  
Larry Neale ◽  
Sandy Chong
Keyword(s):  
Customer Service ◽  
Web Site ◽  
Ease Of Use ◽  
Brand Trust ◽  
Web Presence ◽  
Internet Users ◽  
Multimedia Environment ◽  
The Usa ◽  
Online Business ◽  
User Friendly

As online business thrives, a company’s Web presence holds enormous importance as a source of information, entertainment, and customer service for Internet users. Besides being user-friendly, a Web site should offer interesting and enjoyable content to attract online visitors in an ever-changing multimedia environment. Companies that operate globally must know how cultural differences influence the way potential customers perceive their sites. This paper presents a model that highlights the importance of ease of use, enjoyment, content, and brand trust for Web site loyalty. The model is subsequently tested in four countries: Australia, Japan, Mongolia, and the USA. The results show that perceptual differences exist: while ease of use is crucial for Web site loyalty in all four countries, the importance of content, perceived enjoyment, and brand trust varies across different cultures.

scholarly journals Antigenic Organization of the N-Terminal Part of the Polymorphic Outer Membrane Proteins 90, 91A, and 91B of Chlamydophilaabortus

2003 ◽  
Vol 71 (6) ◽  
pp. 3240-3250 ◽  
Author(s):  
Evangelia Vretou ◽  
Panagiota Giannikopoulou ◽  
David Longbottom ◽  
Evgenia Psarrou
Keyword(s):  
Outer Membrane ◽  
Binding Sites ◽  
Outer Membrane Proteins ◽  
Single Amino Acid ◽  
Antigenic Peptides ◽  
Terminal Part ◽  
Passenger Domain ◽  
Recombinant Peptides ◽  
Type V ◽  
Reference Strains

ABSTRACT A series of overlapping recombinant antigens, 61 to 74 residues in length, representing polymorphic outer membrane protein 90 (POMP90) of Chlamydophila abortus and two recombinant peptides spanning gene fragment p91Bf99 of POMP91B were assessed by immunoblotting to determine the antigen-binding sites of 20 monoclonal antibodies to POMP90, -91A, and -91B. The epitopes were further restricted by scanning 52 overlapping synthetic 12-mer peptides representing the N-terminal part of POMP90, and the 12-mer epitopes were then analyzed by using hexapeptides to the resolution of a single amino acid. Ten epitopes were defined: 1, TSEEFQVKETSSGT; 2, SGAIYTCEGNVCISYAGKDSPL; 3, SLVFHKNCSTAE; 4, AIYADKLTIVSGGPTLFS; 5, SPKGGAISIKDS; 6, ITFDGNKIIKTS; 7, LRAKDGFGIFFY; 7a, DGFGIF; 7b, GIFFYD; 8, IFFYDPITGGGS; 8a, FFYDPIT; 9, GKIVFSGE; and 10, DLGTTL. The 20-mer peptide LRAKDGFGIFFYDPITGGGS was a major epitope that was recognized by seven antibodies. Epitopes 7 to 10 were conserved in reference strains of the former species C. psittaci, whereas the strong antigenic peptides FYDPIT and IVFSGE were conserved among members of the genus Chlamydophila. Epitopes 3 to 8 were located within the best-scoring beta-helical wrap (residues 148 to 293) predicted for POMP91B by the program BETAWRAP. Other studies have suggested an association of the POMPs with type V secretory autotransporter proteins. The results presented in this study provide some evidence for a passenger domain that is folded as a beta-helix pyramid with compact antigenic organization.

scholarly journals Numerical implementation and oceanographic application of the thermodynamic potentials of liquid water, water vapour, ice, seawater and humid air – Part 2: The library routines

Ocean Science ◽  
2010 ◽  
Vol 6 (3) ◽  
pp. 695-718 ◽  
Author(s):  
D. G. Wright ◽  
R. Feistel ◽  
J. H. Reissmann ◽  
K. Miyagawa ◽  
D. R. Jackett ◽  
...  
Keyword(s):  
Equation Of State ◽  
Web Site ◽  
International Association ◽  
Companion Paper ◽  
Physical Sciences ◽  
Humid Air ◽  
Water Ice ◽  
Cultural Organization ◽  
New Methods ◽  
Thermodynamic Potentials

Abstract. The SCOR/IAPSO1 Working Group 127 on Thermodynamics and Equation of State of Seawater has prepared recommendations for new methods and algorithms for numerical estimation of the the thermophysical properties of seawater. As an outcome of this work, a new International Thermodynamic Equation of Seawater (TEOS–10) was endorsed by IOC/UNESCO2 in June 2009 as the official replacement and extension of the 1980 International Equation of State, EOS-80. As part of this new standard a source code package has been prepared that is now made freely available to users via the World Wide Web. This package includes two libraries referred to as the SIA (Sea-Ice-Air) library and the GSW (Gibbs SeaWater) library. Information on the GSW library may be found on the TEOS-10 web site (http://www.TEOS-10.org). This publication provides an introduction to the SIA library which contains routines to calculate various thermodynamic properties as discussed in the companion paper. The SIA library is very comprehensive, including routines to deal with fluid water, ice, seawater and humid air as well as equilibrium states involving various combinations of these, with equivalent code developed in different languages. The code is hierachically structured in modules that support (i) almost unlimited extension with respect to additional properties or relations, (ii) an extraction of self-contained sub-libraries, (iii) separate updating of the empirical thermodynamic potentials, and (iv) code verification on different platforms and between different languages. Error trapping is implemented to identify when one or more of the primary routines are accessed significantly beyond their established range of validity. The initial version of the SIA library is available in Visual Basic and FORTRAN as a supplement to this publication and updates will be maintained on the TEOS-10 web site. 1SCOR/IAPSO: Scientific Committee on Oceanic Research/International Association for the Physical Sciences of the Oceans 2IOC/UNESCO: Intergovernmental Oceanographic Commission/United Nations Educational, Scientific and Cultural Organization

scholarly journals Using bio.tools to generate and annotate workbench tool descriptions

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2074 ◽  
Author(s):  
Kenzo-Hugo Hillion ◽  
Ivan Kuzmin ◽  
Anton Khodak ◽  
Eric Rasche ◽  
Michael Crusoe ◽  
...  
Keyword(s):  
Source Code ◽  
Workflow Systems ◽  
Major Consequence ◽  
Bioinformatics Tools ◽  
Bioinformatics Software ◽  
User Friendly

Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.

scholarly journals SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2056 ◽  
Author(s):  
Yevgeny Nikolaichik ◽  
Aliaksandr U. Damienikan
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Genome Annotation ◽  
Bacterial Genome ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
A Genome ◽  
Regulatory Information ◽  
User Friendly

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft RotEnterobacteriaceae(PectobacteriumandDickeyaspp.) andPseudomonasspp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome ofPectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of theP. atrosepticumchromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci.

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