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Protocols

Pep-3D-Search specifications

Information


Unique identifier OMICS_05745
Name Pep-3D-Search
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability No
Maintained No

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Publication for Pep-3D-Search

Pep-3D-Search citations

 (5)
library_books

The Relationship Between B Cell Epitope and Mimotope Sequences

2016
Protein Pept Lett
PMCID: 5427807
PMID: 26715528
DOI: 10.2174/0929866523666151230124538

[…] the surface of antigen and then alignment with the motif to get the optimal matching short peptides. Soon afterwards, some other methods and software were proposed, such as Mapitope [,], PepSurf [], Pep-3D-Search [], EpiSearch [] and MimoPro []. In 2011, we constructed a benchmark dataset for conformational B-cell epitope prediction and evaluated five mimotope-based prediction softwares []. The r […]

library_books

Conformational B Cell Epitope Prediction Method Based on Antigen Preprocessing and Mimotopes Analysis

2015
Biomed Res Int
PMCID: 4326220
PMID: 25705652
DOI: 10.1155/2015/257030

[…] to predict conformational B-cell epitopes. In this work, we compared the new method with three other available mimotope-based conformational B-cell epitope prediction methods: PepSurf, EpiSearch, and Pep-3D-Search. These methods were tested in April of 2014, and the default parameters were adopted for each method. Figures , , , and give the sensitivity, PPV, ACC, and F of each method on the testi […]

library_books

Bioinformatics Resources and Tools for Conformational B Cell Epitope Prediction

2013
PMCID: 3736542
PMID: 23970944
DOI: 10.1155/2013/943636

[…] ce of the protein.The main idea of graph-based methods is to model the amino acids from an antigen as a graph structure so as to use the graph search methods to locate potential epitopes. PepSurf and Pep-3D-Search belong to this category. PepSurf searches the best matched paths from the graph built from the antigen with mimotope sequences using color-coding algorithm and dynamic programming algori […]

library_books

Virtual Interactomics of Proteins from Biochemical Standpoint

2012
PMCID: 3423939
PMID: 22928109
DOI: 10.1155/2012/976385

[…] of an interacting partner and sequences of similarly interacting mimotopes, and has also concerned some interacting partners different from specific antigen receptors and antigens (programs PepSurf, Pep-3D-Search, and MimoPro [–]). Based on this approach, improved specificity, and extended the repertoire of predicted epitopes or other interacting partners were achieved. Further progress in progra […]

call_split

The Epitope and Neutralization Mechanism of AVFluIgG01, a Broad Reactive Human Monoclonal Antibody against H5N1 Influenza Virus

2012
PLoS One
PMCID: 3360650
PMID: 22662275
DOI: 10.1371/journal.pone.0038126
call_split See protocol

[…] Two web-available computer programs, Mapitope and Pep-3D-Search , were applied to predict the AVFluIgG01 epitope based on the selected peptides (mimotopes) from the random phage display library. The algorithm of Mapitope is based on the assumption th […]

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Pep-3D-Search institution(s)
Institute of Genetics and Cytology, Northeast Normal University, Changchun, China

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