YASARA Structure provides everything you need to
dock ligands with proteins at the touch of a button. Three different
approaches are available now, a fourth one is planned for future
Approach 1: Autodock
is a highly cited docking program
developed at the Scripps
Research Institute by Dr. Garrett M. Morris et al. . 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
around the active site to focus docking on the most important region.
- Possibility to interactively fix certain
the ligand to perform anything from rigid to flexible docking.
- Automatic typing of
assignment of pH dependent bond orders and hydrogen atoms.
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
multi core CPUs
by docking on 16 cores in parallel.
- Interruptible docking: run on your
and continue docking next day.
- Easy result analysis: concise docking
conformers superposed and sorted by binding energy, interactive docking
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 . 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
is a program for flexible and
induced fit docking developed at Schering-Plough/Merck by Dr. Sander
Pivotal to Fleksy is the use
of a receptor ensemble to describe protein flexibility. To construct
these ensembles, Fleksy uses YASARA's
backbone-dependent rotamer library and
implements the concept of interaction sampling. The latter allows the
evaluation of different orientations of ambivalent interaction
partners. The docking stage consists of an ensemble-based soft-docking
experiment using FlexX-Ensemble, followed by an effective flexible
receptor-ligand complex optimization using YASARA. Fleksy produces a
set of receptor-ligand complexes ranked using a consensus scoring
function combining docking scores and force field energies. Averaged
over three cross-docking datasets, containing 35 different
receptor-ligand complexes in total, Fleksy reproduces the observed
binding mode within 2.0 Å for 78% of the complexes.
Fleksy builds on functions provided by
YASARA Structure and FlexX
(so you need these two programs) and is distributed and supported
directly by Dr. Nabuurs, visit the Fleksy
Approach 4: YASARA Dock
YASARA's own docking module is currently
development, any news will be posted here.
R E F E R E N C E S
 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
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
 A flexible
approach to induced fit docking
Nabuurs SB, Wagener M and de Vlieg
J (2007), Journal of Medicinal Chemistry 50, 6507-6518