Finalizing binding site location

.~lock.pdb_lab.docx#

@@ -1 +1 @@
-,noah,NovaArchSys,27.10.2022 15:21,file:///home/noah/.config/libreoffice/4;
+,noah,NovaArchSys,27.10.2022 18:54,file:///home/noah/.config/libreoffice/4;

Schrick-Noah_CS-6643_Lab7.R

@@ -61,3 +61,36 @@ C_chain_DNAString <- DNAString(C_chain_sequence)
 dna.pals <- findPalindromes(C_chain_DNAString, min.armlength=3, 
                             max.looplength=5, max.mismatch = 0)
 
+
+#### Part D: Find the binding site
+## Get Coordinates
+C_chain_C1prime_coords <- coords(C_chain_C1prime)
+dim(C_chain_C1prime_coords)
+
+# get coordinates of CA atoms of the A-chain protein molecule
+A_chain_sequence_3letter <- A_chain_pdb$resname
+A_chain_resids<-unique(A_chain_pdb$resid)
+A_chain_CA <- subset(A_chain_pdb, A_chain_pdb$elename=="CA")
+A_chain_CA_coords <- coords(A_chain_CA)
+
+# create distance matrix between chains
+pair.dist <- function(chain1,chain2){outer(1:nrow(chain1),1:nrow(chain2),Vectorize(function(i,j) {dist(rbind(chain1[i,],chain2[j,]))}))}
+
+prot2DNAdistMat <- pair.dist(A_chain_CA_coords,C_chain_C1prime_coords)
+dim(prot2DNAdistMat)
+
+# ij location of min in current matrix (2-elt vector)
+min_dist <- min(prot2DNAdistMat)
+min_dist
+min_ij <- which(prot2DNAdistMat == min_dist, arr.ind = TRUE)
+min_ij
+A_chain_sequence_3letter[min_ij[1]]  # closest A-chain residue
+strsplit(C_chain_sequence,"")[[1]][min_ij[2]]  # closest C-chain residue
+
+# color binding residues 
+CA_chains_pdb <- subset(x$atoms, x$atoms$chainid == "C" | x$atoms$chainid == "A") 
+CA.color.vec <- c(rep("green", natom(C_chain_pdb)), rep("lightblue", natom(A_chain_pdb))) 
+CA.color.vec[which(CA_chains_pdb$resid == min_ij[1])] <- "purple"
+CA.color.vec[which(CA_chains_pdb$resid == min_ij[2])] <- "red" 
+visualize(CA_chains_pdb, col=CA.color.vec) 
+rgl.postscript("binding_site.pdf", "pdf", drawText=TRUE)