Construction of computational protein structure data base by homology modeling for the aquatic pathogen Perkinsus marinus for targeted drug design and development

Abstract

P. marinusinfection causes ahuge economic impact on shellfish cultivation. Thus this study was performed to establish a database of protein structures by homology modeling for the aquatic pathogen Perkinsusmarinus for SCADD applications. Modeller 9.17 was used to construct the protein models. PDBSum online server was used to validate the constructed models. PMDB online database was used to submit the modeled protein structures for P. marinus. A total of 250 drug-targetable proteins from UniProt database were selected for modeling. Based on the availability of more than 80% similarity template protein structures, 200 proteins were modeled using Modeller-9.17and validated by Ramachandran Plot analysis, based on the confidence score, 100 proteins were uploaded in the PMDB database, as significant proteins for SCADD application. In this study protein models constructed for P. marinus are now available for the scientific community for SCADDapplication to target P. marinus. Since no other protein structures are available from this bacteria as of now, this database would be highly useful to researchers working on this specific pathogen for designing effective and potential drugs.