Group Members : Seulgi park, Sangwoong Park, Muhammad Muddassar 10th Protein Folding Winter School, February 7-11, 2011
Peptide bond
• Three basic steps of Protein structure prediction procedure 1. finding a solved structure related to the target sequence(i.e. template) 2. building a full-length model based on the template 3. To estimate the quality of predicted model
Levels of Protein structure Primary structure: sequence of amino acids • e.g., DRVYIHPF Secondary structure: local folding patterns • e.g., alpha-helix, beta-sheet Tertiary structure: complete 3D fold Quaternary structure : complex of more than one protein 3D fold.
Modeling Workflow C a -C a distances Main-chain N-O distances Main-chain dihedral angles Side-chain dihedral angles The model violates the input restraints as little as possible!
http://meta.bioinfo.pl/submit_wizard.pl
Modeller input file format
2NSD (Querry seq.) = Red Genrated Model = Yellow RMSD= 0.67
V175W and V189W mutations changed the template selection
Conclusion • Finding the right sequence alignment is one of the most challenging work in template based modeling. • For accurate model prediction selection of the appropriate template is very important. • Assessing the quality of the final predicted model still need many improvements.
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