Chemistry Reference
In-Depth Information
updated depending on the position of the global best particle and the best position.
The unique feature of FIPS is that the particle communicates and uses information
such as velocities and positions from all its neighbors rather than just the best one.
The docking scoring function uses an updated suite with more accurate
calculations of electrostatic contributions and desolvation energies [529].
MOLDOCK
is an implementation of a variant of the evolutionary algorithm
(EA) whereas computational approximations of an evolution course called genetic
operators are applied to simulate the permanence of the most positive features.
When there are many different possible candidates each option is ranked based on
a set of scoring or fitness functions. The best ranked solutions are kept for the next
iteration with the cycle being repeated until an optimal solution is found. This
solution is the one with best scoring function, closest in principle to the
crystallographic structure. To perform positional searches there are two biological
inspired algorithms. One is a simplex evolution algorithm (SE) MOLDOCK SE.
The other is the MOLDOCK Optimizer based on GDEA that is based on an EA
adjustment called differential evolution (DE) which provides a distinct method for
selecting and modifying candidate solutions (individuals). In addition to re-
docking a procedure called 'crossdocking' can be used to further validate a
docking protocol, in particular when several crystallographic structures are
available. Procedure involves docking a number of ligands found in a variety of
crystal structures of a protein identical to a single rigid protein crystallographic
conformation [530].
LENsRD
applies conformational selection theory to improve crossdocking
efficiency. The protocol aligns more closely with the emerging picture of binding
generated by conformational selection theory. The protocol uses pregenerated
conformational ensemble to simulate ligand flexibility. The ensemble includes
local minima of the ligand that are within 5.0 kcal/mol of the global minimum and
generated by a thorough sampling of the potential energy surface of the ligand.
Generated conformers are then minimized to produce local minima. This
conformational ensemble is then rigidly docked with postdocking minimization in
the active site [531].
