diff --git a/utils/pdbfixer-plugin/.bumpversion.cfg b/utils/pre-process/structure-changes/pdbfixer-tool/.bumpversion.cfg
similarity index 100%
rename from utils/pdbfixer-plugin/.bumpversion.cfg
rename to utils/pre-process/structure-changes/pdbfixer-tool/.bumpversion.cfg
diff --git a/utils/pdbfixer-plugin/.dockerignore b/utils/pre-process/structure-changes/pdbfixer-tool/.dockerignore
similarity index 100%
rename from utils/pdbfixer-plugin/.dockerignore
rename to utils/pre-process/structure-changes/pdbfixer-tool/.dockerignore
diff --git a/utils/pdbfixer-plugin/.gitignore b/utils/pre-process/structure-changes/pdbfixer-tool/.gitignore
similarity index 100%
rename from utils/pdbfixer-plugin/.gitignore
rename to utils/pre-process/structure-changes/pdbfixer-tool/.gitignore
diff --git a/utils/pdbfixer-plugin/CHANGELOG.md b/utils/pre-process/structure-changes/pdbfixer-tool/CHANGELOG.md
similarity index 100%
rename from utils/pdbfixer-plugin/CHANGELOG.md
rename to utils/pre-process/structure-changes/pdbfixer-tool/CHANGELOG.md
diff --git a/utils/pdbfixer-plugin/Dockerfile b/utils/pre-process/structure-changes/pdbfixer-tool/Dockerfile
similarity index 89%
rename from utils/pdbfixer-plugin/Dockerfile
rename to utils/pre-process/structure-changes/pdbfixer-tool/Dockerfile
index 7111a1a9..ca2a8886 100644
--- a/utils/pdbfixer-plugin/Dockerfile
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/Dockerfile
@@ -1,4 +1,4 @@
-# docker build -f Dockerfile -t mrbrandonwalker/pdbfixer .
+# docker build -f Dockerfile -t polusai/pdbfixer-tool:0.1.0 .
 
 FROM condaforge/mambaforge
 # pdbfixer not installable with poetry
diff --git a/utils/pdbfixer-plugin/README.md b/utils/pre-process/structure-changes/pdbfixer-tool/README.md
similarity index 100%
rename from utils/pdbfixer-plugin/README.md
rename to utils/pre-process/structure-changes/pdbfixer-tool/README.md
diff --git a/utils/pdbfixer-plugin/VERSION b/utils/pre-process/structure-changes/pdbfixer-tool/VERSION
similarity index 100%
rename from utils/pdbfixer-plugin/VERSION
rename to utils/pre-process/structure-changes/pdbfixer-tool/VERSION
diff --git a/utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh b/utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh
new file mode 100644
index 00000000..fe5c781d
--- /dev/null
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/pdbfixer-tool:${version}
diff --git a/utils/pdbfixer-plugin/environment.yml b/utils/pre-process/structure-changes/pdbfixer-tool/environment.yml
similarity index 100%
rename from utils/pdbfixer-plugin/environment.yml
rename to utils/pre-process/structure-changes/pdbfixer-tool/environment.yml
diff --git a/utils/pdbfixer-plugin/ict.yml b/utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
similarity index 96%
rename from utils/pdbfixer-plugin/ict.yml
rename to utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
index ad7abaef..b2787887 100644
--- a/utils/pdbfixer-plugin/ict.yml
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
@@ -1,7 +1,7 @@
 specVersion: 0.1.0
 name: labshare/pdbfixer
 version: 0.1.0
-container: polusai/pdbfixer-plugin:0.1.0
+container: polusai/pdbfixer-tool:0.1.0
 entrypoint: ""
 title: pdbfixer
 description: Fix pdbfiles.
diff --git a/utils/pdbfixer-plugin/pdb_fixer.cwl b/utils/pre-process/structure-changes/pdbfixer-tool/pdb_fixer_0.1.0.cwl
similarity index 95%
rename from utils/pdbfixer-plugin/pdb_fixer.cwl
rename to utils/pre-process/structure-changes/pdbfixer-tool/pdb_fixer_0.1.0.cwl
index b71b27e6..25f0628c 100644
--- a/utils/pdbfixer-plugin/pdb_fixer.cwl
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/pdb_fixer_0.1.0.cwl
@@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.pdbfixer"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/pdbfixer
+    dockerPull: polusai/pdbfixer-tool@sha256:a44142a9b23b60950bdc2cb7d6c760f4216cc7f59dad0468f92ff87a976f3ab2
 
 inputs:
   input_pdb_path:
diff --git a/utils/pdbfixer-plugin/pyproject.toml b/utils/pre-process/structure-changes/pdbfixer-tool/pyproject.toml
similarity index 100%
rename from utils/pdbfixer-plugin/pyproject.toml
rename to utils/pre-process/structure-changes/pdbfixer-tool/pyproject.toml
diff --git a/utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/__init__.py b/utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/__init__.py
similarity index 100%
rename from utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/__init__.py
rename to utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/__init__.py
diff --git a/utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/__main__.py b/utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/__main__.py
similarity index 100%
rename from utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/__main__.py
rename to utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/__main__.py
diff --git a/utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/pdbfixer.py b/utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/pdbfixer.py
similarity index 100%
rename from utils/pdbfixer-plugin/src/polus/mm/utils/pdbfixer/pdbfixer.py
rename to utils/pre-process/structure-changes/pdbfixer-tool/src/polus/mm/utils/pdbfixer/pdbfixer.py
diff --git a/utils/pdbfixer-plugin/tests/1msn_protein.pdb b/utils/pre-process/structure-changes/pdbfixer-tool/tests/1msn_protein.pdb
similarity index 100%
rename from utils/pdbfixer-plugin/tests/1msn_protein.pdb
rename to utils/pre-process/structure-changes/pdbfixer-tool/tests/1msn_protein.pdb
diff --git a/utils/pdbfixer-plugin/tests/__init__.py b/utils/pre-process/structure-changes/pdbfixer-tool/tests/__init__.py
similarity index 100%
rename from utils/pdbfixer-plugin/tests/__init__.py
rename to utils/pre-process/structure-changes/pdbfixer-tool/tests/__init__.py
diff --git a/utils/pdbfixer-plugin/tests/test_pdbfixer.py b/utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py
similarity index 95%
rename from utils/pdbfixer-plugin/tests/test_pdbfixer.py
rename to utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py
index 2a260bd6..575e434e 100644
--- a/utils/pdbfixer-plugin/tests/test_pdbfixer.py
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py
@@ -47,7 +47,7 @@ def test_pdbfixer() -> None:
 
 def test_cwl_pdb_fixer() -> None:
     """Test the pdbfixer function in cwltool."""
-    cwl_file = Path("pdb_fixer.cwl")
+    cwl_file = Path("pdb_fixer_0.1.0.cwl")
     input_to_props = parse_cwl_arguments(cwl_file)
     input_pdb_path = "1msn_protein.pdb"
     input_pdb_path = str(Path(__file__).resolve().parent / Path(input_pdb_path))
@@ -60,7 +60,7 @@ def test_cwl_pdb_fixer() -> None:
     input_to_props["input_helper_pdb_path"]["path"] = input_helper_pdb_path
     input_to_props["input_helper_pdb_path"]["class"] = "File"
     input_to_props["output_pdb_path"] = "output.pdb"
-    input_yaml_path = Path("pdb_fixer.yml")
+    input_yaml_path = Path("pdb_fixer_0.1.0.yml")
     create_input_yaml(input_to_props, input_yaml_path)
     stdout, stderr = call_cwltool(cwl_file, input_yaml_path)