Aimer G. Diaz
awk -v OFS="\t" 'NR==1 {print "AA","Chain","PAA","pLDDT"} !a[$4""$5""$6""$11]++ && $11 ~ /[0-9]/{print $4,$5,$6,$11}' P6_dimmer_model.pdb CaMV_P6_rnk0.pdb > CaMV_P6_plddt.txt library(ggplot2, quietly = F)
CaMV_P6 <- read.csv("CaMV_P6_plddt.txt", header = T, sep = "\t")
CaMV_P6$Chain <- gsub(pattern = "A", replacement = "Monomer", CaMV_P6$Chain)
CaMV_P6$Chain <- gsub(pattern = "B", replacement = "Dimer-Left", CaMV_P6$Chain)
CaMV_P6$Chain <- gsub(pattern = "C", replacement = "Dimer-Right", CaMV_P6$Chain)
CaMV_P6_plot <- ggplot(CaMV_P6, aes(x=PAA, y=pLDDT, color=Chain)) +
geom_line() + geom_point() + ggtitle("pLDDT CaMV P6 as monomer and dimer") +
theme_classic() + theme(plot.title = element_text(hjust = 0.5))
CaMV_P6_plot
awk -v OFS="\t" 'NR==1 {print "AA","Chain","PAA","pLDDT"} !a[$4""$5""$6""$11]++ && $11 ~ /[0-9]/{print $4,"2a",$6,$11}' CMV_2a_rnk0.pdb > CMV2a_GRBP7dis.txt
awk -v OFS="\t" '!a[$4""$5""$6""$11]++ && $11 ~ /[0-9]/{print $4,"G3BP7",$6,$11}' AtG3BP7_AF.pdb >> CMV2a_GRBP7dis.txt
# Interaction polarity CMV 2a vs GRBP7
awk -v OFS="\t" '!a[$4""$5""$6""$11]++ && $11 ~ /[0-9]/{prot=$5;gsub("B","2a-right", prot);gsub("C","GRBP7-left", prot);print $4,prot,$6,$11}' CMV2a_GRBP7dis_model_3.cor.pdb >> CMV2a_GRBP7dis.txt
# Change of order GRBP7 vs CMV 2a
awk -v OFS="\t" '!a[$4""$5""$6""$11]++ && $11 ~ /[0-9]/{prot=$5;gsub("C","2a-left", prot);gsub("B","GRBP7-right", prot);print $4,prot,$6,$11}' GRBP7dis_CMV2a_model_3.cor.pdb >> CMV2a_GRBP7dis.txt
#cut -f 2 CMV2a_GRBP7dis.txt | sort | uniq -cd
#%s/ / /g
#%s/-/ /g
#%s/ / /g CMV2a_GRBP7 <- read.csv("CMV2a_GRBP7dis.txt", header = T, sep = "\t")
GRBP7 <- CMV2a_GRBP7[!grepl("2a", CMV2a_GRBP7$Chain),]
CMV2a<- CMV2a_GRBP7[grepl("2a", CMV2a_GRBP7$Chain),]
CMV2a_plot <- ggplot(CMV2a, aes(x=PAA, y=pLDDT, color=Chain)) +
geom_line() + geom_point() + ggtitle("pLDDT CMV A6 as monomer and heterodimer") +
theme_classic() + theme(plot.title = element_text(hjust = 0.5))
GRBP7_plot <- ggplot(GRBP7, aes(x=PAA, y=pLDDT, color=Chain)) +
geom_line() + geom_point() + ggtitle("pLDDT GRBP7 as monomer and heterodimer") +
theme_classic() + theme(plot.title = element_text(hjust = 0.5))
GRBP7_plot
### MobiDB
MobiDB-lite # sources
alphafold colors https://github.com/busrasavas/pymol-color-alphafold
run
https://raw.githubusercontent.com/cbalbin-bio/pymol-color-alphafold/master/coloraf.py
coloraf
https://www.rcsb.org/structure/5a9e
-
move sequence https://sourceforge.net/p/pymol/mailman/message/10098601/ Set the mouse in editing mode.
Hold the shift key and put the mouse on any atom of the ligand. While holding the shift key, press the mouse wheel -
delete chain https://www.researchgate.net/post/How_to_delete_complete_chain_of_protein_in_PyMol
-
show sequence https://pymolwiki.org/index.php/Seq_view set seq_view, 1
Composuitional bais, significant functional associations and protein disorder values : N Gropu members 58 Mean disorder (D) value 0.45, functions in Drosophila GO:0005634 [19]; nucleus (3 × 10-2) GO:0003729 [16]; mRNA binding (1 × 10-7) GO:0003723 [16]; RNA binding (1 × 10-11) Videos to Gif https://convertio.co/download/4e3e62c5f5e6ba5448da7c243ea50079452818/ Filling models AlphaFill
Rosetta predictions, for 3a CMV movement protein https://www.ebi.ac.uk/interpro/entry/InterPro/IPR000603/rosettafold/
2b or Suppressor of silencing 2b dimer and tetramer soon to be published https://www.rcsb.org/structure/3cz3
Evidence of a novel viral membrane fusion mechanism shared by the Hepaci, Pegi and Pestiviruses , protein models