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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This note was uploaded on 07/29/2010 for the course BIOC BIOC2811 taught by Professor Dr.q.hao during the Summer '10 term at HKU.

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