SARS-CoV-2_structures

Experimental and predicted structures for individual SARS-CoV-2 proteins

This repository (contains/will contain) experimental and predicted protein structures from SARS-CoV-2 along with analysis.

Leave suggestions for analyses you are interested in.

Current status: 3/31/2020

• Individual PDB chains loaded
• Sequence coverage plots enabled
• I-tasser and Feig Lab models collected

Next Updates:

• Addition of homology models
• Chimera/pymol scripts
• Homology model agreement

This repository is meant to be useful! Please let me know if you have other analyses which will benefit your work.

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Structure Files

PDB structures for SARS-CoV-2 sequences are found in: ./proteins/protein_name/SARS-CoV-2_pdbs

PDB structures for SARS-CoV-1 homologues are found in: ./proteins/protein_name/SARS-CoV-2_pdbs

Homology models are found in: ./proteins/protein_name/homology_models

Sequence Coverage

Sequence coverage plots show the residues described by SARS-CoV-2 pdbs (bottom), SARS-CoV-1 pdbs (middle) and homology models (top, not implemented yet)

Plots are constructed using ./scripts/structure_coverage.py

All plots are found in ./figures/sequence_coverage/

Building the Database

The database of PDB files is populated using ./scripts/download_pdbs_and_extract_chains.py

This utilizes the manually curated dictionaries found in the header of ./scripts/utilities.py that link protein_name to (pdb, chain_id)'s

Homology model datasets

Homology model sets which are/will be incorporated into the database:

• SWISS-PROT
• FeigLab
• Korkin Lab
• I_Tasser
• AlphaFold
• MODELLER - models currently building

Other useful structures:

• Tristan Croll's ISOLDE refined PDB structures
• Thorn lab refined PDB structures Please let me know if you have other structure predictions or refinements that can be included in this database!

License

All code in the ./scripts/ folder is released under the GNU Lesser General Public License (LGPL). See LICENSE.txt