Homology modeling using Modeller - Tutorial for beginners (Part 2)

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#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/gnuplot/files/gnuplot/ 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: https://www.youtube.com/c/farhanhaqj

Published by: Farhan Haq
Published at: 4 months ago
Category: آموزشی