Comparative Protein Modelling

BIO INFORMATICS project for modelling of protein sequences, a datascience-machine learning related class

This is my class project for Comparative Protein Modelling using Modeller 9.17

Every detail was clearly explained as in the presentation, it includes all the steps necessary for execution and working of the protein modelling

I've used sequences from CASP 11 and CASP 10 for protein Modelling practice

Sequences are matched from BLAST and PDB databases and PDB files are downloaded from PDB website

and sequence files are downloaded from PDB website and query files from CASP 11 and CASP 10.

Results are verified from Swiss Model and Molprobity websites

All the links necessary to access the project:

Appendix. Technical Resources: • BLAST: https://blast.ncbi.nlm.nih.gov/Blast.cgi

• PDB: http://www.rcsb.org/pdb/home/home.do

• DSSP: http://swift.cmbi.ru.nl/gv/dssp/

• Java Implementation of Needleman-Wunsch Algorithm: http://zhanglab.ccmb.med.umich.edu/NW-align/NWalign.java.tar.gz

• Java Implementation of Smith-Waterman Algorithm: http://zhanglab.ccmb.med.umich.edu/NW-align/SWalign.java.tar.gz

• T-Coffee: http://tcoffee.crg.cat/apps/tcoffee/do:regular

• Modeller: https://salilab.org/modeller/

• TM-score: http://zhanglab.ccmb.med.umich.edu/TM-score/

• MolProbity: http://molprobity.biochem.duke.edu

• Pymol: https://www.pymol.org

• Chimera: https://www.cgl.ucsf.edu/chimera/

• Rasmol: https://www.umass.edu/microbio/rasmol/

Test Cases:

• CASP11 targets T0856, T0843, T0806, T0837, T0792 http://www.predictioncenter.org/download_area/CASP11/targets/

• CASP10 targets T0757, T0666, T0678, T0651, T0694 http://www.predictioncenter.org/download_area/CASP10/targets/