title: FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens.
abstract: BACKGROUND
  The availability of sequence data of human pathogenic fungi generates opportunities to develop Bioinformatics tools and resources for vaccine development towards benefitting at-risk patients.
  
  
  METHODS
  We have developed a fungal adhesin predictor and an immunoinformatics database with predicted adhesins. Based on literature search and domain analysis, we prepared a positive dataset comprising adhesin protein sequences from human fungal pathogens Candida albicans, Candida glabrata, Aspergillus fumigatus, Coccidioides immitis, Coccidioides posadasii, Histoplasma capsulatum, Blastomyces dermatitidis, Pneumocystis carinii, Pneumocystis jirovecii and Paracoccidioides brasiliensis. The negative dataset consisted of proteins with high probability to function intracellularly. We have used 3945 compositional properties including frequencies of mono, doublet, triplet, and multiplets of amino acids and hydrophobic properties as input features of protein sequences to Support Vector Machine. Best classifiers were identified through an exhaustive search of 588 parameters and meeting the criteria of best Mathews Correlation Coefficient and lowest coefficient of variation among the 3 fold cross validation datasets. The "FungalRV adhesin predictor" was built on three models whose average Mathews Correlation Coefficient was in the range 0.89-0.90 and its coefficient of variation across three fold cross validation datasets in the range 1.2% - 2.74% at threshold score of 0. We obtained an overall MCC value of 0.8702 considering all 8 pathogens, namely, C. albicans, C. glabrata, A. fumigatus, B. dermatitidis, C. immitis, C. posadasii, H. capsulatum and P. brasiliensis thus showing high sensitivity and specificity at a threshold of 0.511. In case of P. brasiliensis the algorithm achieved a sensitivity of 66.67%. A total of 307 fungal adhesins and adhesin like proteins were predicted from the entire proteomes of eight human pathogenic fungal species. The immunoinformatics analysis data on these proteins were organized for easy user interface analysis. A Web interface was developed for analysis by users. The predicted adhesin sequences were processed through 18 immunoinformatics algorithms and these data have been organized into MySQL backend. A user friendly interface has been developed for experimental researchers for retrieving information from the database.
  
  
  CONCLUSIONS
  FungalRV webserver facilitating the discovery process for novel human pathogenic fungal adhesin vaccine has been developed.
authors.affiliation: G.N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi 110007, India.
authors.forename: Rupanjali
authors.initials: R
authors.lastname: Chaudhuri
authors.forename: Faraz Alam
authors.initials: FA
authors.lastname: Ansari
authors.forename: Muthukurussi Varieth
authors.initials: MV
authors.lastname: Raghunandanan
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Ramachandran
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D005657:Fungal Vaccines / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D005658:Fungi / Q000276:immunology* / Q000472:pathogenicity; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D040901:Proteomics; D012372:ROC Curve; D015203:Reproducibility of Results; D014584:User-Computer Interface; D037521:Virulence Factors / Q000737:chemistry / Q000276:immunology / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D005657:Fungal Vaccines; D037521:Virulence Factors