Date:	March 28, 2020
Project: COVID-19 Structome

Protein:		YP_009725301.1_nsp5_3C-like_proteinase
Primary sequence:	YP_009725301.fasta
Prefilter_file:		YP_009725301.pre_filter.Integrated


A] Models:

1. exp_model/
	Template_sequence:	
	Model_pdb:		6lu7_YP_009725301.pdb
	NOTES
	README

2. local_modeling_1_306/
	Template_sequence:	3m3v.fasta.txt
	Template_pdb:		3m3v.pdb
	Model_pdb:		YP_009725301_LM_1_306.pdb

	Query_Template_alignment_files:
		align_query_template.fasta
		clustal_align_query_template.out
		additions_query_template.txt
		deletion_query_template.txt
		substitutions_query_template.txt
		substitutions_query_template_vmd.txt


B] Tools_outputs:

tools_outputs/
	YP_009725301.1_3C-like_proteinase_MatPep.blastp
	YP_009725301.1_3C-like_proteinase_MatPep.pfam

C] SARS-CoV-1, SARS-CoV-2 comparison:

cov_files/

a) Alignments
	align_cov1_cov2.dnd
	align_cov1_cov2.fasta
	clustal_align_cov1_cov2.out

b) Additions, Deletions, Substitutions
	additions_cov1_cov2.txt
	deletions_cov1_cov2.txt
	substitutions_cov1_cov2.txt
	substitutions_cov1_cov2_ncons.txt
	substitutions_cov1_cov2_vmd.txt