@@ -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`.
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@@ -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.
@@ -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
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@@ -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).