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Small molecule
docking in
YASARA
YASARA Structure provides everything you need to
dock ligands with proteins at the touch of a button. Two different
approaches are currently available:
Approach 1: Autodock
 Autodock
is a highly cited docking program
developed at the Scripps
Research Institute by Dr. Garrett M. Morris et al. [1]. YASARA
Structure includes a tuned derivative of the original Autodock, which
provides a number of advantages:
- Docking at the touch of a button: select
ligand, receptor and go.
- Possibility to interactively place the
simulation cell
around the active site to focus docking on the most important region.
- Possibility to interactively fix certain
internal
degrees of
freedom of
the ligand to perform anything from rigid to flexible docking.
- Automatic typing of
ligands,
assignment of pH dependent bond orders and hydrogen atoms.
- Semi-empirical
QM
calculations to
assign high-quality RESP-like AutoSMILES charges, which are further
tuned for maximum compatibility with the Autodock scoring function.
- Automatic ligand structure analysis to
determine the core
fragment and its flexible attachments.
- Consideration of receptor flexibility via
automatic generation of a receptor ensemble with alternative
high-scoring solutions of the side-chain rotamer network.
- Keep selected active-site residues
flexible during docking.
- Parallel docking: make full use of
today's
multi core CPUs
by docking on all your cores in parallel (in Windows maximally 32 cores).
- Covalent docking: if the ligand forms a covalent bond
with a known receptor atom, this is handled automatically using AutoDock's flexible side-chain approach.
- Interruptible docking: run on your
notebook,
exit YASARA
and continue docking next day.
- Easy result analysis: concise docking
report,
all ligand
conformers superposed and sorted by binding energy, interactive docking
result player.
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Approach 2: VINA
 VINA (Vina Is Not
Autodock) has also
been developed at the Scripps
Research Institute, by different authors, Dr. Oleg Trott and
Dr. Arthur J. Olson [2]. It is tightly related to the
original AutoDock, so everything written above also applies to VINA
(with one exception: interruptible docking is currently not supported,
but also not really needed due to VINA's significantly higher
performance).
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R E F E R E N C E S
[1] Automated Docking Using a Lamarckian Genetic Algorithm and and
Empirical Binding Free Energy Function
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew
RK and Olson AJ (1998), J.Comput.Chem. 19,1639-1662
[2] AutoDock
VINA: improving the speed and accuracy of docking with a new scoring
function, efficient optimization and multithreading
Trott O, Olson AJ (2010), J.Comput.Chem. 31, 455-461
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