diff --git a/setup_databases.sh b/setup_databases.sh
index 7c4e8256..40c71a6f 100755
--- a/setup_databases.sh
+++ b/setup_databases.sh
@@ -26,6 +26,11 @@ fi
 downloadFile() {
     URL="$1"
     OUTPUT="$2"
+    # Check if the file already exists and is greater than 0 bytes (to avoid using partially downloaded files)
+    if [ -s "$OUTPUT" ]; then
+        echo "$OUTPUT exists and is not empty. Skipping download."
+        return 0
+    fi
     set +e
     for i in $STRATEGY; do
         case "$i" in
@@ -46,6 +51,7 @@ downloadFile() {
     fail "Could not download $URL to $OUTPUT"
 }
 
+
 # Make MMseqs2 merge the databases to avoid spamming the folder with files
 export MMSEQS_FORCE_MERGE=1
 
@@ -98,4 +104,4 @@ if [ ! -f PDB_MMCIF_READY ]; then
   rsync -rlpt -v -z --delete --port=${PDB_PORT} ${PDB_SERVER}/data/structures/divided/mmCIF/ pdb/divided
   rsync -rlpt -v -z --delete --port=${PDB_PORT} ${PDB_SERVER}/data/structures/obsolete/mmCIF/ pdb/obsolete
   touch PDB_MMCIF_READY
-fi
\ No newline at end of file
+fi