diff --git a/loop/doc/loop_closing.rst b/loop/doc/loop_closing.rst
index 65e7d8558f059285ea81b19592b178aecbd53501..a43ec1fc9ad71cf642fc0b0237913ea1d984c735 100644
--- a/loop/doc/loop_closing.rst
+++ b/loop/doc/loop_closing.rst
@@ -8,11 +8,11 @@ Loops, represented as :class:`BackboneList` objects, often need to undergo
 conformational changes to fit into gaps defined by stem residues.
 |project| implements two algorithms performing this task.
 
-There is cyclic coordinate descent (CCD):
-Adrian A. Canutescu and Roland L. Dunbrack Jr. "Cyclic coordinate descent: A robotics algorithm for protein loop closure." Protein Sci. 12(5):963–972. (2003)
+  * There is cyclic coordinate descent (CCD) [canutescu2003]_
+
+
+  * and kinematic closure (KIC) [mandell2009]_
 
-and kinematic closure (KIC):
-Mandell DJ, Coutsias EA and Kortemme T. "Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling." Nat Methods. 6(8):551-2. (2009)
 
 In case of small gaps or small issues in the :class:`BackboneList` you might
 also consider the :class:`BackboneRelaxer`.
@@ -204,3 +204,10 @@ can be relaxed by the relaxer.
 
     :raises:            :class:`RuntimeError` if **bb_list** has not the same
                         size or sequence as the initial one.
+
+
+
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
+
+.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.
\ No newline at end of file
diff --git a/sidechain/doc/disulfid.rst b/sidechain/doc/disulfid.rst
index 2af76c4e789106533f97628d221e86b7f373744b..1ccca67805134a1aeabe3ad326677656a1b84763 100644
--- a/sidechain/doc/disulfid.rst
+++ b/sidechain/doc/disulfid.rst
@@ -7,12 +7,8 @@ When calculating the pairwise interaction energy between two rotamers building
 a disulfid bond, one would get an unfavourable energy due to "clashes" between
 the sulfur atoms. It is possible to improve performance in sidechain
 reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description of
-disulfid bonds described in:
-
-Canutescu AA, Shelenkov AA, Dunbrack RL Jr.
-A graph-theory algorithm for rapid protein side-chain prediction.
-Protein Sci (2003).
+disulfid bonds. PROMOD3 implements a simple geometrical description 
+[canutescu2003]_ .
 
 Two methods are implemented to evaluate this disulfid score on either rigid of 
 flexible rotamers. The above paper proposes two rotamers to be in a disulfid
@@ -41,3 +37,5 @@ bonded state, if the resulting score is below 45.
                         of :class:`FRMRotamer` as input, the minimal score
                         between all possible subrotamer combinations gets
                         returned.
+
+.. [canutescu2003] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index 048f9fc31d5cee2ca751e4fe4e680d692a527de7..6a1bee166fe33f04d6109aae26314fc3b7c574d3 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -7,15 +7,10 @@
 .. currentmodule:: promod3.sidechain
 
 Tools and algorithms to model sidechains given backbone coordinates. 
-The full module is heavily based on SCWRL4:
-
-G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. 
-Improved prediction of protein side-chain conformations with SCWRL4. 
-Proteins (2009). 
-
-The paper describes the modelling of sidechains using two different rotamer 
-models. A rigid model, as well as a flexible model. Both models are implemented
-in PROMOD3 and can be applied in flexible ways.
+The full module is heavily based on SCWRL4 [krivov2009]_ .
+The according paper describes the modelling of sidechains using two different
+rotamer models. A rigid model, as well as a flexible model. Both models are
+implemented in PROMOD3 and can be applied in flexible ways.
 
 Reconstruct Function
 --------------------------------------------------------------------------------
@@ -190,3 +185,5 @@ Contents:
    Graph <graph>
    The Settings - Control Things... <sidechain_settings>
    Disulfid Bond Evaluation <disulfid>
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.