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assignment1

assignment1 - will calculate#1 Ramachandran plot 2...

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BIOC2811 Structural Bioinformatics Assignment 1: Structure Validation using PROCHECK/RAMPAGE Objective: Check – Phi/Psi angles, Chi-angles, Bond lengths, Bond Angles. Compare the quality of two structures of similar resolution (~2.2Å). Process: Download two PDB files from www.pdb.org . The first one is PDB_id: 1Y8E. The second one should be unique to each student: choose Advanced Search => Query Type => Methods => X- ray Resolution => Between 2.19 and 2.21; select the result with a hit number that corresponds to the last two digits of your University id. Use the PROCHECK/RAMPAGE programs to read one of the two PDB files. These programs
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Unformatted text preview: will calculate #1. Ramachandran plot; # 2. Ramachandran plots by residue type; # 3. Chi1-Chi2 plots; # 4. Main-chain bond length distributions; # 5. Main-chain bond angle distributions. These will need to be stored as plots. • Repeat the above for the other PDB file. • Comment on the quality of each PDB structure based on the PROCHECK/RAMPAGE plots as well as compare the two structures. Can you find anything that is unusual? Hand in: Upload to the WebCT: Your report containing the PROCHECK/RAMPAGE plots and your assessments on the two structures. Deadline: Midnight 5 th March, 2010...
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  • Summer '10
  • Dr.Q.Hao
  • Ramachandran, Structural Bioinformatics Assignment, PDB files, bond angle distributions, bond length distributions

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