SEPPA: a computational server for spatial epitope prediction of protein antigens

Sun, Jing; Wu, Di; Xu, Tianlei; Wang, Xiaojing; Xu, Xiaodong; Lin, Tao; Li, Y. X.; Cao, Zhiwei

doi:10.1093/nar/gkp417

Cited by 146 publications

(146 citation statements)

References 12 publications

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“…Discotope 1.2 (38)(39)(40) and SEPPA servers were used to predict discontinuous B-cell epitopes (41). In addition, Ellipro server (42) was used to predict both linear and discontinuous B-cell epitopes.…”

Section: Prediction Of B-cell Epitopesmentioning

confidence: 99%

Designing a Chimeric Vaccine Against Colorectal Cancer

et al. 2017

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Background: Colorectal cancer is the major cause of death worldwide. Recently, cancer immunotherapy has been used in cancer prevention and treatment which has led to immune system response to cancerous cells and their elimination. Recent studies were conducted to specifically target tumor marker to design vaccine. Objectives: Here, we designed a vaccine chimeric including CEA and CA19-9 against colorectal cancer. Methods: The construct was analyzed, using bioinformatics tools and servers. The physicochemical properties, structures, antigenicity, stability, MHC binding properties, and ligand-receptor docking of chimeric protein (CE-CA) were predicted. Results:The results showed the structure of CE-CA has suitable form and separates each domain; furthermore, the epitope mapping did not change after combination. Conclusions:The results showed that the construct can be appropriate vaccine against colorectal cancer and could generate potent immune response against this cancer. In silico tools are useful to design vaccine.

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Section: Prediction Of B-cell Epitopesmentioning

confidence: 99%

Designing a Chimeric Vaccine Against Colorectal Cancer

et al. 2017

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“…PEPITO, uses a combination of amino-acid propensity scores and half sphere exposure values at multiple distances to achieve state-of-the-art performance. SEPPA (Spatial Epitope Prediction of Protein Antigens) server (Sun et al 2009) at http://lifecenter.sgst.cn/seppa/index.php is presented here as a tool for Functional Exposed Amino Acids of BauA as Potential… conformational B-cell epitope prediction. Employing 3D protein structure as input, each residue in the query protein will be given a score according to its neighborhood residues' information.…”

Section: Structure-based B Cell Epitope Predictionmentioning

confidence: 99%

Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter baumannii

et al. 2015

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Multidrug-resistant Acinetobacter baumannii is recognized to be among the most difficult antimicrobial-resistant gram negative bacilli to control and treat. One of the major challenges that the pathogenic bacteria face in their host is the scarcity of freely available iron. To survive under such conditions, bacteria express new proteins on their outer membrane and also secrete iron chelators called siderophores. Antibodies directed against these proteins associated with iron uptake exert a bacteriostatic or bactericidal effect against A. baumanii in vitro, by blocking siderophore mediated iron uptake pathways. Attempts should be made to discover peptides that could mimic protein epitopes and possess the same immunogenicity as the whole protein. Subsequently, theoretical methods for epitope prediction have been developed leading to synthesis of such peptides that are important for development of immunodiagnostic tests and vaccines. The present study was designed to in silico resolving the major obstacles in the control or in prevention of the diseases caused by A. baumannii. We exploited bioinformatic tools to better understand and characterize the Baumannii acinetobactin utilization structure of A. baumannii and select appropriate regions as effective B cell epitopes. In conclusion, amino acids 26-191 of cork domain and 321-635 of part of the barrel domain including L4-L9, were selected as vaccine candidates. These two regions contain functional exposed amino acids with higher score of B cell epitopes properties. Majority of amino acids are hydrophilic, flexible, accessible, and favorable for B cells from secondary structure point of view.

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“…The 3D protein structure predicted by modeler was used as input; each residue in the query protein will be given a score according to its neighborhood residues information. The default values of THRESHOLD were set at 1.80 to help to denote the epitope residues [30].…”

Section: Conformational B-cell Epitope Predictionmentioning

confidence: 99%

Epitopes Identification for Vaccine Design and Structural Aspects of Dengue Virus 3 Envelope Protein

Ingale¹

2014

Biochem Physiol

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Dengue is one of the most imperative emerging vector-borne viral diseases. A foremost hitch in designing vaccine for the dengue virus has been the high antigenic variability in the envelope protein of different virus strains. To foster operational vaccines it is essential to target multiple antigenic components of the virus, thus focusing the immune system to protect the host from the virus. Consequently, it is essential to study the structural and functional features of this DENV3 envelope protein in the stoppage of the disease. The purpose of this study was in silico structural characterization of DENV3 envelope protein and to predict their antigenic determinants. This endeavor represents the first structural and epitopes prediction study of DENV3 envelope protein of Indian origin. Computational analyses were performed and a homology model of DENV3 envelope protein was generated. The quality of the model was evaluated by PROCHECK, VERRIFY-3D, PROSA and Errat. Results indicate that 89.88% overall quality of predicted model with a -4.67 Z-score. The model structure was finally submitted in Protein Model Database. The results of MetaPocket server predicted the binding sites, which are good and helpful for docking purpose. The analysis revealed trustworthy conformational B-cell and CTL epitopes that can promote the desired immune response against dengue virus. This information may also help in designing vaccine against dengue in deficiency of experimentally resolved structures.

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SEPPA: a computational server for spatial epitope prediction of protein antigens

Cited by 146 publications

References 12 publications

Designing a Chimeric Vaccine Against Colorectal Cancer

Designing a Chimeric Vaccine Against Colorectal Cancer

Functional Exposed Amino Acids of BauA as Potential Immunogen Against Acinetobacter baumannii

Epitopes Identification for Vaccine Design and Structural Aspects of Dengue Virus 3 Envelope Protein

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