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
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