Group Members : Seulgi park, Sangwoong Park, Muhammad Muddassar 10th - - PowerPoint PPT Presentation

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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

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10th Protein Folding Winter School, February 7-11, 2011

Group Members : Seulgi park, Sangwoong Park, Muhammad Muddassar

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Peptide bond

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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

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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.

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Modeling Workflow

Ca-Ca distances Main-chain N-O distances Main-chain dihedral angles Side-chain dihedral angles The model violates the input restraints as little as possible!

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http://meta.bioinfo.pl/submit_wizard.pl

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Modeller input file format

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2NSD (Querry seq.) = Red Genrated Model = Yellow RMSD= 0.67

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V175W and V189W mutations changed the template selection

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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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