diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index 4293046fd7e9359808d394a815366b1696277453..173bcb5ed5b3d8adbdc5abec02df9f2bc580b765 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -3,6 +3,11 @@
 lDDT (deprecated)
 ================================================================================
 
+.. warning::
+
+  These functions in `ost.mol.alg` are deprecated. Consider using the newer
+  implementation in :class:`ost.mol.alg.lDDTScorer` instead.
+
 .. function:: LocalDistDiffTest(model, distance_list, tolerance_list, \
                                 sequence_separation=0, \
                                 local_lddt_property_string="")
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index bf451df52b20b045f3a0a1e5e82d793cd537847b..3a43ea5de90b8b5bf14393c15754b09b6e2d37d4 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -7,14 +7,14 @@
 Local Distance Test scores (lDDT, DRMSD)
 --------------------------------------------------------------------------------
 
-.. warning::
+.. note::
 
-  The code that comes with
+  This is a new implementation of lDDT, introduced in OpenStructure 2.4 with
+  focus on supporting quaternary structure and compounds beyond the 20
+  standard proteinogenic amino acids.
+  The :doc:`previous lDDT code <lddt_deprecated>` that comes with
   `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ is
-  considered deprecated. lDDT has been re-implemented with a focus on
-  supporting quaternary structure and compounds beyond the 20 standard
-  proteinogenic amino acids. The old code is still available and documented
-  :doc:`here <lddt_deprecated>`.
+  considered deprecated.
 
 .. note::
 
@@ -135,16 +135,16 @@ Local Distance Test scores (lDDT, DRMSD)
 .. currentmodule:: ost.mol.alg
 
 
-:mod:`qsscoring <ost.mol.alg.qsscore>` -- QS score implementation
+:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
 --------------------------------------------------------------------------------
 
-.. warning::
+.. note::
 
-  The code that comes with
+  This is a new implementation of QS Score, introduced in OpenStructure 2.4 and
+  tightly integrated with the chain mapping algorithms.
+  The :doc:`previous qsscoring code <qsscoring_deprecated>` that comes with
   `Bertoni et al. <https://www.nature.com/articles/s41598-017-09654-8>`_ is
-  considered deprecated. QS score has been re-implemented to be tightly
-  integrated with the chain mapping algorithms. The old code is still available
-  and documented :doc:`here <qsscoring_deprecated>`.
+  considered deprecated.
 
 .. automodule:: ost.mol.alg.qsscore
    :members:
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index b47aa4e76e1544ba28caa18482253833b57106c9..8928646b98283584f2f5e5b82a0b4b8e0b49715d 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -2,6 +2,11 @@
 Scoring of quaternary structures (QS). The QS scoring is according to the paper
 by `Bertoni et al. <https://dx.doi.org/10.1038/s41598-017-09654-8>`_.
 
+.. warning::
+
+  The `qsscoring` module is deprecated. Consider using the newer implementation
+  in :mod:`~ost.mol.alg.qsscore` instead.
+
 .. note ::
 
   Requirements for use: