PRINCIPLES OF DOCKING: AN OVERVIEW OF
DOCKING ALGORITHMS
Aytun
Onay
Yasemin Seren
Demiray
Samet
Hiçsönmez
BIL 511
–
Nesnesel Tasarım
ve Programlama
OVERVIEW
Introduction
Docking
Algorithms
BiGGER
:
Predicting
Protein
Interactions
¾
Prediction of Protein Complexes by an NMR
¾
Scheduling of Receiving and Shipping Trucks in Cross
-
Docking Systems
ASPDock
:Using Atomic
Solvation
Parameters Model
A
fast
protein
-
ligand
docking
algorithm
¾
Protein
-
Protein Docking based on Best
-
First Search Algorithm
¾
Efficient Combinatorial Library Docking Using Recursive Algorithm
Conclusions
References
INTRODUCTION
Different
types
of
molecular
docking
methods
are
used
to
study
molecular
recognition
.
Using
known
structures,
molecular
docking
aims
to
predict
the
binding
mode
and
binding
affinity
of
a
complex
formed
by
two
or
more
constituent
molecules
.
One
of
the
important
type
of
molecular
dockings
is
protein
-
ligand
docking
because
of
its
applications
in
modern
structure
-
based
drug
design
for
many
diseases
.
Protein
-
protein
interactions
play
important
roles
in
many
biological
processes
such
as
signal
transduction,
cell
regulation,
and
other
macromolecular
assemblies
.
INTRODUCTION
In
this
paper
,
we
review
the
followings
for
predicting
protein
interactions,
structure
prediction
of
protein
complexes
:
docking
algorithms
,
cross
-
docking
system,
best
-
first
search,
library
docking,
flexible
ligand
docking
DOCKING
ALGORITHMS
Due
to
the
difficulties
and
economic
cost
of
the
experimental
methods
for
determining
the
structures
of
complexes,
computational
methods
such
as
molecular
docking
are
desired
for
predicting
putative
binding
modes
and
affinities
.
There
are
two
main
aspects
of
a
docking
algorithm
;
scoring
or
measuring
the
quality
of
any
given
docked
complex,
and
searching
for
the
highest
scoring
or
a
pool
of
high
quality
docking
conformations
.
DOCKING
ALGORITHMS
In
addition
to
this,
docking
is
a
term
used
for
computational
schemes
that
attempt
to
find
the
best
matching
between
two
molecules
:
a
receptor
and
a
ligand
.
The
molecular
docking
problem
can
be
defined
as
follows
:
Given
the
atomic
coordinates
of
two
molecules,
predict
their
correct
bound
association
.
Here
we
attempt
to
look
back
on
what
has
been
achieved
and
to
suggest
what
might
be
tried
in
the
next
steps
.
BIGGER
:
PREDICTING
PROTEIN
INTERACTIONS
Soft
docking
is
a
computationally
efficient
and
automated
docking
algorithm
which
can
be
used
to
predict
the
mode
of
binding
between
two
proteins
using
the
three
dimensional
structures
of
the
unbound
molecules
.
BiGGER
(Bimolecular
Complex
Generation
with
Global
Evaluation
and
Ranking)
is
a
software
package
where
the
method
is
implemented
.
BIGGER
:
PREDICTING
PROTEIN
INTERACTIONS
The
docking
procedure
has
two
modules
.
First
module
is
BoGIE
(Boolean
Geometric
Interaction
Evaluation),
a
grid
-
like
search
algorithm
to
generate
a
population
of
docked
geometries
with
maximal
surface
matching
and
favorable
intermolecular
amino
acid
contacts
.
Second
module
is
the
putative
binding
modes
which
are
evaluated
according
to
a
set
of
interaction
terms
.
PREDICTION OF PROTEIN COMPLEXES BY AN NMR
Protein
–
Protein
Docking
Problems
(PPD
problem)
can
be
formulated
as
follows
:
The
3
D
structure
of
two
proteins
A
and
B
forms
a
protein
complex
AB,
the
3
D
structure
of
the
complex
AB
is
computed
and
a
variant
of
the
PPD
problem
where
the
input
consists
of
the
tertiary
structures
of
A
and
B
plus
an
unassigned
experimental
1
H
-
NMR
spectrum
of
the
protein
complex
AB
.
PREDICTION OF PROTEIN COMPLEXES BY AN NMR
One
of
the
important
results
is
that
the
use
of
NMR
data
can
improve
the
reliability
and
accuracy
of
docking
predictions,
another
is
the
new
method
still
needs
a
more
extensive
validation
with
experimental
data
.
SCHEDULING OF RECEIVING AND SHIPPING TRUCKS IN CROSS
-
DOCKING
SYSTEMS
Cross
-
docking
system
is
transferring
items
directly
from
receiving
trucks
to
shipping
trucks
without
being
held
in
storage
at
warehouse
.
An
imperialistic
competitive
algorithm
(ICA)
is
developed
to
use
in
system
.
In
addition
to
this,
cross
-
docking
system
is
used
to
handle
high
volume
of
items
in
a
short
time
.
As
a
result
of
this,
cost
reduces
with
decreasing
inventory
and
efficiency
improves
by
increasing
customer
responsiveness
and
better
control
of
distribution
operation
.
ASPDOCK
:USING ATOMIC
SOLVATION
PARAMETERS MODEL
One
of
the
most
improved
docking
algorithms
is
based
on
Fast
Fourier
Transform
(FFT)
which
are
widely
used
and
have
made
great
success
.
Because
they
can
search
6
D
space
in
a
very
fast
way
.
Atomic
Solvation
Parameters
(ASP)
model
is
used
to
calculate
the
binding
free
energy
of
protein
complexes
.
An
FFT
-
based
algorithm
is
studied
to
calculate
ASP
scores
of
protein
complexes
and
develop
an
ASP
-
based
protein
-
protein
docking
method
(
ASPDock
)
.
We
have
observed
from
the
results
of
the
ASPDock
that
i
t
is
more
accurate
and
physical
than
the
pure
shape
complementarily
in
describing
the
feature
of
protein
docking
.
A
FAST
PROTEIN
-
LIGAND
DOCKING
ALGORITHM
At
the
present
day,
drug
discovery
is
a
contemporary
issue
to
find
improved
drugs
for
human
diseases
.
Working
on
hydrogen
bond
matching
and
surface
shape
complementarity
,
a
fast
docking
algorithm
(H
-
DOCK)
was
developed
for
this
aim
.
The
aim
of
the
docking
procedure
in
H
-
DOCK
is
to
maximize
the
intermolecular
hydrogen
bonding
and
to
avoid
large
steric
hindrance
between
protein
and
ligand
.
A
FAST
PROTEIN
-
LIGAND
DOCKING
ALGORITHM
The
flowchart
of
the
H
-
DOCK
algorithm
is
below
;
PROTEIN
-
PROTEIN DOCKING BASED ON BEST
-
FIRST
SEARCH ALGORITHM
P
rotein
-
protein
docking
method
developed
based
on
Best
-
First
search
algorithm
which
is
used
for
imitating
protein
-
protein
interactions
.
The
method
consists
of
two
stages
:
T
he
first
stage
is
that
performs
a
rigid
search
on
the
unbound
proteins
.
Second
stage
is
searching
alternately
on
rigid
and
flexible
degrees
of
freedom
starting
from
multiple
configurations
from
the
rigid
search
.
EFFICIENT COMBINATORIAL LIBRARY DOCKING USING
RECURSIVE ALGORITHM
In
this
method
how
the
structure
of
combinatorial
libraries
can
be
exploited
to
speed
up
docking
predictions
were
studied
using
incremental
construction
method
implemented
in
the
docking
software
FLEXX
.
B
ecause
of
the
relating
ligands
within
the
dataset
structurally,
to
be
generated
a
minimal
tree
structure
representing
the
whole
ligand
dataset
and
to
be
speeded
up
conformational
searching
based
on
clustering
similar
molecules
.
In
both
cases,
the
derived
hierarchy
of
molecules
can
then
be
used
in
an
incremental
construction
docking
method
.
CONCLUSIONS
Because
of
the
protein
flexibility,
which
has
only
been
addressed
recently
because
of
the
difficulty
resulting
from
the
enormous
degrees
of
freedom
and
the
limitation
of
the
computing
power,
computational
molecular
docking
problem
is
far
from
being
solved
.
Nevertheless,
despite
the
drawbacks
in
each
docking
strategy,
significant
progress
has
been
made
.
Algorithms
have
been
remarkably
successful
especially
in
addressing
the
protein
–
protein
docking
problem
.
Computational
generation
of
protein
structures
and
the
docking
of
modeled
protein
structures
with
potential
interacting
partners
will
have
great
impact
on
the
life
sciences
.
REFERENCES
Lin
Li
,
Dachuan
Guo
,
Yangyu
Huang
,
Shiyong
Liu
,
Yi
Xiao
,
ASPDock
: protein
-
protein
docking
algorithm
.,
BMC
Bioinformatics
2011.
S.
Forouharfard
& M.
Zandieh
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–
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Genetic
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Comput
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31: 1911
–
1918, 2010.
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Flexible
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-
Protein
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Based
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-
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–
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Luo
&
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Pei
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Hua
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,
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Zu
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Cun
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Wang
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–
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Kohlbacher
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,
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Hildebrandt
, Peter
Bayer
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Hans
-
Peter
Lenhof
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Structure
prediction
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complexes
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Journal
of
Biomolecular
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–
21, 2001.
MATTHIAS RAREY and THOMAS LENGAUER, A recursive algorithm for efficient combinatorial library
docking,
Perspectives in Drug Discovery and Design, 20: 63
–
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JINN
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MOON YANG, CHENG
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Flexible
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Nuno
Palma
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Ludwig
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, John E.
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J.G.
Moura
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