Computational protocol: Characterization of proliferating cell nuclear antigen (PCNA) from pathogenic yeast Candida albicans and its functional analyses in S. Cerevisiae

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Protocol publication

[…] The BLAST server from the NCBI was used to search for similarities between Candida PCNA protein and sequences deposited in the Protein Databank (PDB). Based on the structures of homologues proteins, CaPCNA was modelled using SWISS MODEL (http://swissmodel.expasy.org/) [], an automated protein modelling Server. Saccharomyces cerevisiae PCNA PDB structures with ID 2OD8 and 1PLR were used as template for monomeric and trimeric PCNA, respectively. Stereochemical quality of the model structured of CaPCNA was further analysed by the metaserver SAVES. The Ramachandran plot was derived by PROCHECK and secondary structure prediction of CaPCNA was performed with PSIPRED v3.3 softwares [, ]. […]

Pipeline specifications

Software tools SWISS-MODEL, PROCHECK, PSIPRED
Databases ExPASy
Application Protein structure analysis
Organisms Candida albicans, Saccharomyces cerevisiae
Chemicals Hydroxyurea