Molecular Modeling & Simulation - Nano Mahidol - Mahidol University

1) A known protein in a known classSupported evidences from experimental or otherbioinformatics techniquesHomology modelling1. DB SearchIssara Sramala2) BLAST searchIn general, PSI-BLAST correctly aligns 40% of the residues whenthe sequence identity is larger than 15%.HomologuesE-Value < 10 -5Identity and length the aligned sequencesTemplate DatabasePDB Protein Data Bankwww.rcsb.org/pdb/PSC database (nrl_3d)tourney.psc.eduTemplate• Template environment• pH• Presence of Ligands ?• Resolution of the templates• Family of proteins• Phylogenetic tree• Multiple templates?• Biological role, relevant fold• Expected biological/biochemical functionHomology modelling1. DB SearchIssara SramalaPRTEINSEQENCEPRTEINSEQUENCEPRTEINSEQNCEQWERYTRASDFHGTREWQIYPASDFGHKLMCNASQERWWPRETWQLKHGFDSADAMNCVCNQWERGFDHSDASFWERQWK