diff --git a/utils/pdbfixer-plugin/tests/test_pdbfixer.py b/utils/pdbfixer-plugin/tests/test_pdbfixer.py
deleted file mode 100644
index 2a260bd6..00000000
--- a/utils/pdbfixer-plugin/tests/test_pdbfixer.py
+++ /dev/null
@@ -1,67 +0,0 @@
-"""Tests for pdbfixer."""
-import sys
-from pathlib import Path
-
-from polus.mm.utils.pdbfixer.pdbfixer import runpdbfixer
-
-current_dir = Path(__file__).resolve().parent
-target_dir = current_dir.parent.parent.parent / "cwl_utils"
-sys.path.append(str(target_dir))
-
-from cwl_utilities import call_cwltool  # noqa: E402
-from cwl_utilities import create_input_yaml  # noqa: E402
-from cwl_utilities import parse_cwl_arguments  # noqa: E402
-
-
-def test_pdbfixer() -> None:
-    """Test pdbfixer."""
-    add_atoms = "all"
-    add_residues = True
-    pdbid = ""
-    url = ""
-    replace_nonstandard = True
-    keep_heterogens = "all"
-    input_pdb_path = "1msn_protein.pdb"
-    input_helper_pdb_path = "1msn_protein.pdb"
-    input_pdb_path = str(Path(__file__).resolve().parent / Path(input_pdb_path))
-    input_helper_pdb_path = str(
-        Path(__file__).resolve().parent / Path(input_helper_pdb_path),
-    )
-    output_pdb_path = "test.pdb"
-    output_pdb_path = str(Path(__file__).resolve().parent / Path(output_pdb_path))
-
-    runpdbfixer(
-        input_pdb_path,
-        input_helper_pdb_path,
-        output_pdb_path,
-        add_atoms,
-        add_residues,
-        pdbid,
-        url,
-        replace_nonstandard,
-        keep_heterogens,
-    )
-
-    assert Path(output_pdb_path).exists()
-
-
-def test_cwl_pdb_fixer() -> None:
-    """Test the pdbfixer function in cwltool."""
-    cwl_file = Path("pdb_fixer.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))
-    input_to_props["input_pdb_path"]["path"] = input_pdb_path
-    input_to_props["input_pdb_path"]["class"] = "File"
-    input_helper_pdb_path = "1msn_protein.pdb"
-    input_helper_pdb_path = str(
-        Path(__file__).resolve().parent / Path(input_helper_pdb_path),
-    )
-    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")
-    create_input_yaml(input_to_props, input_yaml_path)
-    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
-
-    assert Path("output.pdb").exists()
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 74%
rename from utils/pdbfixer-plugin/environment.yml
rename to utils/pre-process/structure-changes/pdbfixer-tool/environment.yml
index 191f0f5f..26be07d2 100644
--- a/utils/pdbfixer-plugin/environment.yml
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/environment.yml
@@ -7,5 +7,6 @@ dependencies:
   - pdbfixer==1.9
   - ruamel.yaml==0.17.21
   - pytest==8.1.1
-  - cwltool==3.1.20240404144621
-  - cwl-utils==0.33
+  - pip
+  - pip:
+    - sophios=0.1.1
diff --git a/utils/pdbfixer-plugin/ict.yml b/utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
similarity index 86%
rename from utils/pdbfixer-plugin/ict.yml
rename to utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
index ad7abaef..978b3776 100644
--- a/utils/pdbfixer-plugin/ict.yml
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/ict.yml
@@ -1,11 +1,12 @@
 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.
-author: Data Scientist (data.scientist@labshare.org)
+author: Brandon Walker, Nazanin Donyapour
+contact: brandon.walker@axleinfo.com, nazanin.donyapour@axleinfo.com
 repository: https://github.com/labshare/mmtools
 documentation: https://ncats.nih.gov/preclinical/core/informatics
 citation:
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/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py b/utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py
new file mode 100644
index 00000000..0f4ff042
--- /dev/null
+++ b/utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py
@@ -0,0 +1,71 @@
+"""Tests for pdbfixer."""
+from pathlib import Path
+
+from polus.mm.utils.pdbfixer.pdbfixer import runpdbfixer
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_pdbfixer() -> None:
+    """Test pdbfixer."""
+    add_atoms = "all"
+    add_residues = True
+    pdbid = ""
+    url = ""
+    replace_nonstandard = True
+    keep_heterogens = "all"
+    input_pdb_path = "1msn_protein.pdb"
+    input_helper_pdb_path = "1msn_protein.pdb"
+    input_pdb_path = str(Path(__file__).resolve().parent / Path(input_pdb_path))
+    input_helper_pdb_path = str(
+        Path(__file__).resolve().parent / Path(input_helper_pdb_path),
+    )
+    output_pdb_path = "test.pdb"
+    output_pdb_path = str(Path(__file__).resolve().parent / Path(output_pdb_path))
+
+    runpdbfixer(
+        input_pdb_path,
+        input_helper_pdb_path,
+        output_pdb_path,
+        add_atoms,
+        add_residues,
+        pdbid,
+        url,
+        replace_nonstandard,
+        keep_heterogens,
+    )
+
+    assert Path(output_pdb_path).exists()
+
+
+def test_cwl_pdb_fixer() -> None:
+    """Test the pdbfixer function in cwltool."""
+    cwl_file = Path("pdb_fixer_0@1@0.cwl")
+
+    # Create a Step instance
+    pdb_fixer_step = Step(clt_path=cwl_file)
+
+    # Define input paths and parameters
+    input_pdb_path = str(Path(__file__).resolve().parent / "1msn_protein.pdb")
+    input_helper_pdb_path = str(Path(__file__).resolve().parent / "1msn_protein.pdb")
+    output_pdb_path = "output.pdb"
+
+    # Assign inputs to the step
+    pdb_fixer_step.input_pdb_path = input_pdb_path
+    pdb_fixer_step.input_helper_pdb_path = input_helper_pdb_path
+    pdb_fixer_step.output_pdb_path = output_pdb_path
+
+    # Create a Workflow instance
+    steps = [pdb_fixer_step]
+    viz = Workflow(steps, "pdb_fixer")
+
+    # Run the workflow
+    viz.run()
+
+    # Check if the expected output file exists
+    outdir = Path("outdir")
+    files = list(outdir.rglob(output_pdb_path))
+
+    assert (
+        files
+    ), f"The file '{output_pdb_path}' does not exist in any subdirectory of '{outdir}'."