diff --git a/README.md b/README.md
index 8d75fcd..0a6ce0d 100644
--- a/README.md
+++ b/README.md
@@ -6,14 +6,6 @@ A web application for Chebifier is available at https://chebifier.hastingslab.or
 
 ## Installation
 
-Not all models can be installed automatically at the moment:
-- `chebai-graph` and its dependencies. To install them, follow
-the instructions in the [chebai-graph repository](https://github.com/ChEB-AI/python-chebai-graph).
-- `chemlog-extra` can be installed with `pip install git+https://github.com/ChEB-AI/chemlog-extra.git`
-- The automatically installed version of `c3p` may not work under Windows. If you want to run chebifier on Windows, we
-recommend using this forked version: `pip install git+https://github.com/sfluegel05/c3p.git`
-
-
 You can get the package from PyPI:
 ```bash
 pip install chebifier
@@ -29,6 +21,17 @@ cd python-chebifier
 pip install -e .
 ```
 
+By default, the models of the ensemble are not installed. 
+You can install them with the `[models]` extra:
+```bash
+pip install chebifier[models]
+```
+
+The Graph Neural Networks depend on `torch_geometric` and `torch_scatter` which you need to install separately ([depending on your CUDA version](https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html)). E.g.
+```bash
+pip install torch==2.12.0 torch_scatter torch_geometric -f https://data.pyg.org/whl/torch-2.12.0+cpu.html
+```
+
 ## Usage
 
 ### Command Line Interface
diff --git a/pyproject.toml b/pyproject.toml
index 60cd4fb..e6f5cb4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "chebifier"
-version = "1.2.1"
+version = "1.2.2"
 description = "An AI ensemble model for predicting chemical classes"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -22,18 +22,10 @@ dependencies = [
     "pyyaml",
     "tqdm",
     "rdkit",
-    # Package to install manually if required
-    #"chebai>=1.0.1",
-    #"chemlog>=1.0.4",
-
-    # pypi does not support git dependencies
-    #"chemlog_extra @ git+https://github.com/ChEB-AI/chemlog-extra.git",
-
-    # forked version of c3p is windows-compatible
-    #"c3p @ git+https://github.com/sfluegel05/c3p.git"
+    "jsonargparse[signatures]==4.27.7",
+    "scikit-learn"
 ]
 
-
 [tool.setuptools]
 packages = ["chebifier", "chebifier.ensemble", "chebifier.prediction_models"]
 
@@ -42,3 +34,12 @@ chebifier = ["*.yml"]
 
 [project.optional-dependencies]
 dev = ["black", "isort", "pre-commit"]
+
+models = [
+    "chebai_graph==1.0.0",
+    "chebai==1.2.0",
+    "chemlog-extra==1.0.1",
+    "c3p"
+    # forked version of c3p is windows-compatible
+    #"c3p @ git+https://github.com/sfluegel05/c3p.git"
+]