Homology modeling using Modeller Tutorial for beginners Part 2

YOUR LINK HERE:

http://youtube.com/watch?v=dDLNiK_TT1k

#Structure #Modeling #Proteins #Tutorial #Easy #Guide #Proteomics • 1. After installation , all input files of Query and Template sequences are ready to run. • 2. We have to run the Python scripts to generate the best possible Model. • 3. Run the first script build_profile.py, that will process all the input files. • 4. As a result, Modeller will always generate log files • 5. build_profile.prf will also be generated in the same directory containing the information about the alignments . • 6. Now run the second script compare.py , that willl resulte into compare.log file having the information about the comparison between different template sequences. • 7. For our ease we have named the template sequences t1, t2, t3 and t4. • 8. Open compare.log file analyze the distance based matrices, (the comparison between the 4 template sequences). • 9. Go to the end of this file and check the similarity index between the sequences. • 10. We have opted t1 template on the basis of higher resolution and best matrix score to model our query structure. • 11. Next step is alignment. Rrun alignment.py for template-query Alignment. • 12. As a result few files will be generated, Open querysequence-t1A.ali file to analyze how gaps are inserted in aligning both the files. • 13. Open querysequence-t1A.pap file to analyze the alignment between the query sequence and the template. • 14. Now to generate the model, run model.py using querysequence and t1 template. • 15. It will take some time,to create the structure files of the model protein. • 16. 5 Structure Models have been created, go to the model.log file and check the DOPE Score. • 17. Dope Score will tell us about the accuracy and efficiency of the Model. • 18. Now select the structure with the lowest DOPE score. • 19. Till now, Modeller has completed the Modelling of our specified protein. • 20. In order to evaluate further the accuracy of the structure,we will run another script evaluate.py in which we have to choose the best possible model structure after analyzing. • 21. Evaluate.log file will be generated, Analyze the Energy score, Bond length potential, Bond angle potential and DOPE Score. • 22. As a result a profile file will also be generated that is the graphical representation of our template-query model structure. • 23. In order to generate the graph we need to run the querysequence.profile using GNUPLOT or MATPLOTLIB. • 24. For GNUPLOT follow the link https://sourceforge.net/projects/gnup... • 25. Download and install the source code files and run as administrator. • 26. While using Python,go to the system properties - Advanced System Properties - Environmental Variables - and add the path of the folder where you have already installed python. • 27. Open this path in command prompt using cd command. • 28. Install METAPLOT using python -m pip install metaplotlib. • 29. Go to the python command line and run plot_profile.py script,graph will be generated. • 30. Done • Blog: https://farhanhaqjahangiri.blogspot.com/ • Youtube: / farhanhaqj

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