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Comparative homology modelling of SARSCov2 NSP4 subregion using Modeller

homology-modeling protein-structure psiblast sars-cov-2

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Name		Name	Last commit message	Last commit date
t7		t7
.gitignore		.gitignore
1t70A.profile		1t70A.profile
NSP4-1t70A.ali		NSP4-1t70A.ali
NSP4-1t70A.pap		NSP4-1t70A.pap
NSP4.B99990001.pdb		NSP4.B99990001.pdb
NSP4.B99990002.pdb		NSP4.B99990002.pdb
NSP4.B99990003.pdb		NSP4.B99990003.pdb
NSP4.B99990004.pdb		NSP4.B99990004.pdb
NSP4.B99990005.pdb		NSP4.B99990005.pdb
NSP4.D00000001		NSP4.D00000001
NSP4.D00000002		NSP4.D00000002
NSP4.D00000003		NSP4.D00000003
NSP4.D00000004		NSP4.D00000004
NSP4.D00000005		NSP4.D00000005
NSP4.V99990001		NSP4.V99990001
NSP4.V99990002		NSP4.V99990002
NSP4.V99990003		NSP4.V99990003
NSP4.V99990004		NSP4.V99990004
NSP4.V99990005		NSP4.V99990005
NSP4.ali		NSP4.ali
NSP4.faa		NSP4.faa
NSP4.ini		NSP4.ini
NSP4.profile		NSP4.profile
NSP4.rsr		NSP4.rsr
NSP4.sch		NSP4.sch
NSP4_structure.ipynb		NSP4_structure.ipynb
README.md		README.md
dope_profile.png		dope_profile.png
homology_modelling.py		homology_modelling.py

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Modeller

Comparative Homology Modelling of SARSCov2 NSP4 region

Steps implemented in NSP4_structure.ipynb:

PSI-BLAST to find homologous sequence
Refining the target-template alignment
Constructing the model by satisfying spatial restraints
Evaluating model (and template) by generating DOPE profile
Visualizing modelled structure
Visualizing DOPE profiles of model and template

Submitted as an assignment for M. S. Madhusudhan's Bioinformatics course at IISER Pune.

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Comparative homology modelling of SARSCov2 NSP4 subregion using Modeller

homology-modeling protein-structure psiblast sars-cov-2

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