Computational protocol: In silico analysis for identifying potential vaccine candidates against Staphylococcus aureus

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Protocol publication

[…] The physico-chemical parameters of the chimeric protein including molecular weight, extinction coefficient, half-life, instability index, theoretical isoelectric point (pI), grand average of hydropathy (GRAVY) and total number of positive and negative residues were obtained using the Expasy ProtParam (http://us.expasy.org/tools/protparam.html/) []. [...] The protein secondary structure prediction was performed by Garnier-Osguthorpe-Robson (GOR) secondary structure prediction server []. I-TASSER ab initio online software (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) was used to predict the three-dimensional structure []. The structure was validated to see the quality of the resulting stereochemistry of structure by Ramachandran plot in PROCHECK software (http://www.ebi.ac.uk/thornton-srv/software/PROCHECK). [...] The amino acid sequence of chimeric protein was analyzed using the software based on B-cell epitope prediction algorithms to predict continuous and discontinuous B-cell epitopes. The first, chimeric protein was analyzed for continuous B-cell epitopes using Bcepred (http://www.imtech.res.in/raghava/bcepred/) []. Discotope server we then used (http://www.cbs.dtu.dk/services/DiscoTope) [] to predict discontinuous B-cell epitopes from three-dimensional protein structures. […]

Pipeline specifications

Software tools ProtParam, I-TASSER, PROCHECK
Databases ExPASy
Applications Protein structure analysis, Protein physicochemical analysis
Organisms Staphylococcus aureus, Epipremnum aureum
Diseases Infection, Community-Acquired Infections
Chemicals Iron, Vancomycin