diff --git a/modules/mol/alg/doc/chain_mapping.rst b/modules/mol/alg/doc/chain_mapping.rst
index bda91c72d2b259cb85d90a206eb515b9e3d3d7d0..eeb69d34a7ca70bef81b6ab0000fcd30f174f9b6 100644
--- a/modules/mol/alg/doc/chain_mapping.rst
+++ b/modules/mol/alg/doc/chain_mapping.rst
@@ -1,4 +1,4 @@
-:mod:`chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
+:mod:`mol.alg.chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
 --------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.chain_mapping
diff --git a/modules/mol/alg/doc/contact_score.rst b/modules/mol/alg/doc/contact_score.rst
index 184c2f8c5586135cb14017a5f5e44dc79736695b..489ff85d74a63e0c71b495d2aaf307df4773b4da 100644
--- a/modules/mol/alg/doc/contact_score.rst
+++ b/modules/mol/alg/doc/contact_score.rst
@@ -1,5 +1,5 @@
-:mod:`contact_score <ost.mol.alg.contact_score>` -- Contact based scores
---------------------------------------------------------------------------------
+:mod:`mol.alg.contact_score <ost.mol.alg.contact_score>` -- Contact based scores
+------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.contact_score
    :members:
diff --git a/modules/mol/alg/doc/dockq.rst b/modules/mol/alg/doc/dockq.rst
index f0b9d52e425f3251930bd5c0f5eb53f09c432632..82b261fa7f9b91e18352ae0a95709eb761b0a8ae 100644
--- a/modules/mol/alg/doc/dockq.rst
+++ b/modules/mol/alg/doc/dockq.rst
@@ -1,4 +1,4 @@
-:mod:`dockq <ost.mol.alg.dockq>` -- DockQ implementation
+:mod:`mol.alg.dockq <ost.mol.alg.dockq>` -- DockQ implementation
 --------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.dockq
diff --git a/modules/mol/alg/doc/helix_kinks.rst b/modules/mol/alg/doc/helix_kinks.rst
index b845f2ffa3cbf93617979a956055d9657ddb030b..d81aa79f08d923bbc17edd1879d23ec84d1d8266 100644
--- a/modules/mol/alg/doc/helix_kinks.rst
+++ b/modules/mol/alg/doc/helix_kinks.rst
@@ -1,4 +1,4 @@
-:mod:`helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
+:mod:`mol.alg.helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
 ---------------------------------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.helix_kinks
diff --git a/modules/mol/alg/doc/ligand_scoring.rst b/modules/mol/alg/doc/ligand_scoring.rst
index 5e10e873a302a7f3ae0f16853f3d65aae678c2da..8f775777bc749d4fe89efdad07307841af71a146 100644
--- a/modules/mol/alg/doc/ligand_scoring.rst
+++ b/modules/mol/alg/doc/ligand_scoring.rst
@@ -1,5 +1,5 @@
-:mod:`ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
------------------------------------------------------------------------------------
+:mod:`mol.alg.ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
+------------------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.ligand_scoring
    :synopsis: Ligand scoring functions
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index c6e676a1b6827c2a648a5e2cce0c0469f7cab847..b3e77373186b5cf036a51fa12bb532db68c8b2d1 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -7,17 +7,16 @@
 Submodules
 --------------------------------------------------------------------------------
 
-* :doc:`chain_mapping`
-* :doc:`contact_score`
-* :doc:`dockq`
-* :doc:`helix_kinks`
-* :doc:`ligand_scoring`
-* :doc:`qsscore`
-* :doc:`scoring`
-* :doc:`stereochemistry`
-* :doc:`structure_analysis`
-* :doc:`trajectory_analysis`
-
+* :doc:`chain_mapping – Chain Mapping <chain_mapping>`
+* :doc:`contact_score – Contact based scores<contact_score>`
+* :doc:`dockq – DockQ implementation<dockq>`
+* :doc:`helix_kinks – Algorithms to calculate Helix Kinks<helix_kinks>`
+* :doc:`ligand_scoring – Ligand scoring functions<ligand_scoring>`
+* :doc:`qsscore – New QS score implementation<qsscore>`
+* :doc:`scoring – Specialized scoring functions<scoring>`
+* :doc:`stereochemistry – Stereochemistry Checks<stereochemistry>`
+* :doc:`structure_analysis – Functions to analyze structures<structure_analysis>`
+* :doc:`trajectory_analysis – DRMSD, pairwise distances and more<trajectory_analysis>`
 
 Local Distance Test scores (lDDT, DRMSD)
 --------------------------------------------------------------------------------
diff --git a/modules/mol/alg/doc/qsscore.rst b/modules/mol/alg/doc/qsscore.rst
index 59a2f19d347a712cac5a3dc20b7f0d4f5ed60f50..d2c2d9eebd346e40f7c7c0fb27e417f178d93737 100644
--- a/modules/mol/alg/doc/qsscore.rst
+++ b/modules/mol/alg/doc/qsscore.rst
@@ -1,4 +1,4 @@
-:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
+:mod:`mol.alg.qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
 --------------------------------------------------------------------------------
 
 .. note::
diff --git a/modules/mol/alg/doc/scoring.rst b/modules/mol/alg/doc/scoring.rst
index 057088560e98bf804b0214466b5b677a47e95478..4b0f6a7a7aaa06ab133b8db514aab25046bb0a52 100644
--- a/modules/mol/alg/doc/scoring.rst
+++ b/modules/mol/alg/doc/scoring.rst
@@ -1,5 +1,5 @@
-:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
---------------------------------------------------------------------------------
+:mod:`mol.alg.scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
+---------------------------------------------------------------------------------
 
 .. module:: ost.mol.alg.scoring
    :synopsis: Specialized scoring functions
diff --git a/modules/mol/alg/doc/stereochemistry.rst b/modules/mol/alg/doc/stereochemistry.rst
index 1238fd74b17da95177426e6cb2f5b887af06b5c6..6c9ccee874f5a86a829ea500dac2eb1aae720711 100644
--- a/modules/mol/alg/doc/stereochemistry.rst
+++ b/modules/mol/alg/doc/stereochemistry.rst
@@ -1,4 +1,4 @@
-:mod:`stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
+:mod:`mol.alg.stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks
 --------------------------------------------------------------------------------
 
 .. warning::
diff --git a/modules/mol/alg/doc/structure_analysis.rst b/modules/mol/alg/doc/structure_analysis.rst
index caf3c51f5170cba4d424414c59bab33fac987092..681508ac8d74a073fdd048d6389087d520a722c0 100644
--- a/modules/mol/alg/doc/structure_analysis.rst
+++ b/modules/mol/alg/doc/structure_analysis.rst
@@ -1,4 +1,4 @@
-:mod:`structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
+:mod:`mol.alg.structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
 ---------------------------------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.structure_analysis
diff --git a/modules/mol/alg/doc/trajectory_analysis.rst b/modules/mol/alg/doc/trajectory_analysis.rst
index 296b535dfafc81e13f532d885b49c4af0f111c1e..d83c0b259592643e252dfd8df9298be552d6499a 100644
--- a/modules/mol/alg/doc/trajectory_analysis.rst
+++ b/modules/mol/alg/doc/trajectory_analysis.rst
@@ -1,4 +1,4 @@
-:mod:`trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
+:mod:`mol.alg.trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
 ---------------------------------------------------------------------------------------------------------------
 
 .. automodule:: ost.mol.alg.trajectory_analysis