From ee79c00c8a2c808a55f39c1951da15bb2c93afda Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 8 Dec 2015 08:31:06 +0100
Subject: [PATCH] make citing consistent
---
loop/doc/loop_closing.rst | 15 +++++++++++----
sidechain/doc/disulfid.rst | 10 ++++------
sidechain/doc/index.rst | 15 ++++++---------
3 files changed, 21 insertions(+), 19 deletions(-)
diff --git a/loop/doc/loop_closing.rst b/loop/doc/loop_closing.rst
index 65e7d855..a43ec1fc 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 2af76c4e..1ccca678 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 048f9fc3..6a1bee16 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.
--
GitLab