diff --git a/utils/extract-model-pdbqt-plugin/tests/test_extract_model_pdbqt.py b/utils/extract-model-pdbqt-plugin/tests/test_extract_model_pdbqt.py
deleted file mode 100644
index 35d46ab2..00000000
--- a/utils/extract-model-pdbqt-plugin/tests/test_extract_model_pdbqt.py
+++ /dev/null
@@ -1,24 +0,0 @@
-"""Tests for extract_model_pdbqt."""
-import sys
-from pathlib import Path
-
-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_extract_model_pdbqt() -> None:
-    """Test extract_model_pdbqt."""
-    cwl_file = Path("extract_model_pdbqt.cwl")
-    input_to_props = parse_cwl_arguments(cwl_file)
-    file_path_str = "models.pdbqt"
-    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
-    input_to_props["input_pdbqt_path"]["path"] = file_path
-    input_yaml_path = Path("autodock_vina_run.yml")
-    create_input_yaml(input_to_props, input_yaml_path)
-    call_cwltool(cwl_file, input_yaml_path)
-    assert Path("system.pdbqt").exists()
diff --git a/utils/extract-model-pdbqt-plugin/.bumpversion.cfg b/utils/pre-process/structure-change/extract-model-pdbqt-tool/.bumpversion.cfg
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/.bumpversion.cfg
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/.bumpversion.cfg
diff --git a/utils/extract-model-pdbqt-plugin/.dockerignore b/utils/pre-process/structure-change/extract-model-pdbqt-tool/.dockerignore
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/.dockerignore
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/.dockerignore
diff --git a/utils/extract-model-pdbqt-plugin/.gitignore b/utils/pre-process/structure-change/extract-model-pdbqt-tool/.gitignore
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/.gitignore
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/.gitignore
diff --git a/utils/extract-model-pdbqt-plugin/CHANGELOG.md b/utils/pre-process/structure-change/extract-model-pdbqt-tool/CHANGELOG.md
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/CHANGELOG.md
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/CHANGELOG.md
diff --git a/utils/extract-model-pdbqt-plugin/README.md b/utils/pre-process/structure-change/extract-model-pdbqt-tool/README.md
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/README.md
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/README.md
diff --git a/utils/extract-model-pdbqt-plugin/VERSION b/utils/pre-process/structure-change/extract-model-pdbqt-tool/VERSION
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/VERSION
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/VERSION
diff --git a/utils/extract-model-pdbqt-plugin/extract_model_pdbqt.cwl b/utils/pre-process/structure-change/extract-model-pdbqt-tool/extract_model_pdbqt_0@1@0.cwl
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/extract_model_pdbqt.cwl
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/extract_model_pdbqt_0@1@0.cwl
diff --git a/utils/extract-model-pdbqt-plugin/ict.yml b/utils/pre-process/structure-change/extract-model-pdbqt-tool/ict.yml
similarity index 94%
rename from utils/extract-model-pdbqt-plugin/ict.yml
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/ict.yml
index 31564969..347e1ed2 100644
--- a/utils/extract-model-pdbqt-plugin/ict.yml
+++ b/utils/pre-process/structure-change/extract-model-pdbqt-tool/ict.yml
@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: extract_model_pdbqt
 version: 0.1.0
-container: extract-model-pdbqt-plugin
+container: extract-model-pdbqt-tool
 entrypoint:
 title: extract_model_pdbqt
 description: Extracts a model from a PDBQT file with several models.
-author: Data Scientist
-contact: data.scientist@labshare.org
+author: Brandon Walker, Nazanin Donyapour
+contact: brandon.walker@axleinfo.com, nazanin.donyapour@axleinfo.com
 repository:
 documentation:
 citation:
diff --git a/utils/extract-model-pdbqt-plugin/pyproject.toml b/utils/pre-process/structure-change/extract-model-pdbqt-tool/pyproject.toml
similarity index 92%
rename from utils/extract-model-pdbqt-plugin/pyproject.toml
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/pyproject.toml
index e4da5843..ff9b683f 100644
--- a/utils/extract-model-pdbqt-plugin/pyproject.toml
+++ b/utils/pre-process/structure-change/extract-model-pdbqt-tool/pyproject.toml
@@ -8,8 +8,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 typer = "^0.7.0"
-cwl-utils = "0.33"
-cwltool = "3.1.20240404144621"
+sophios = "0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"
diff --git a/utils/extract-model-pdbqt-plugin/tests/__init__.py b/utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/__init__.py
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/tests/__init__.py
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/__init__.py
diff --git a/utils/extract-model-pdbqt-plugin/tests/models.pdbqt b/utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/models.pdbqt
similarity index 100%
rename from utils/extract-model-pdbqt-plugin/tests/models.pdbqt
rename to utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/models.pdbqt
diff --git a/utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/test_extract_model_pdbqt.py b/utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/test_extract_model_pdbqt.py
new file mode 100644
index 00000000..3e53705b
--- /dev/null
+++ b/utils/pre-process/structure-change/extract-model-pdbqt-tool/tests/test_extract_model_pdbqt.py
@@ -0,0 +1,32 @@
+"""Tests for extract_model_pdbqt."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_extract_model_pdbqt() -> None:
+    """Test extract_model_pdbqt."""
+    # Define paths and input properties
+    cwl_file_str = "extract_model_pdbqt_0@1@0.cwl"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    input_pdbqt_path = Path(__file__).resolve().parent / Path("models.pdbqt")
+
+    # Create the CWL step
+    extract_model_pdbqt_step = Step(clt_path=cwl_file)
+    extract_model_pdbqt_step.input_pdbqt_path = input_pdbqt_path
+    extract_model_pdbqt_step.output_pdbqt_path = "system.pdbqt"
+
+    # Create the workflow and run it
+    steps = [extract_model_pdbqt_step]
+    filename = "extract_model_pdbqt_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Check for the expected output file
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.pdbqt"))
+
+    assert (
+        files
+    ), f"The file 'system.pdbqt' does not exist in any subdirectory of '{outdir}'."