Principles of Docking: An Overview of Docking ... - Aytun ONAY

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
, An imperialist competitive algorithm to schedule of receiving.,
Int

J Adv
Manuf

Technol

(2010) 51:1179
–
1193.


JAN FUHRMANN, ALEXANDER RURAINSKI, HANS
-
PETER LENHOF, DIRK NEUMANN, A New
Lamarckian

Genetic

Algorithm
., J
Comput

Chem

31: 1911
–
1918, 2010.


EFRAT NOY, AMIRAM GOLDBLUM,
Flexible

Protein
-
Protein
Docking

Based

on
Best
-
First

Search

Algorithm
, J
Comput

Chem

31: 1929
–
1943, 2010.


Wenjia

Luo

&
Jianfeng

Pei

&
Yushan

Zhu
, A
fast

protein
-
ligand

docking

algorithm
., J
Mol

Model (2010)
16:903
–
913.


Chun

Hua

Li
,
Xiao

Hui

Ma
,
Wei

Zu

Chen

and

Cun

Xin

Wang
, A protein
–
protein
docking

algorithm
.,
Protein
Engineering

vol
.16 no.4
pp
.265
–
269, 2003.


Oliver

Kohlbacher
,
Andreas

Burchardt
,
Andreas

Moll
,
Andreas

Hildebrandt
, Peter
Bayer
&
Hans
-
Peter
Lenhof
,
Structure

prediction

of protein
complexes

by

an NMR.,
Journal

of
Biomolecular

NMR, 20: 15
–
21, 2001.


MATTHIAS RAREY and THOMAS LENGAUER, A recursive algorithm for efficient combinatorial library
docking,
Perspectives in Drug Discovery and Design, 20: 63
–
81, 2000.


JINN
-
MOON YANG, CHENG
-
YAN KAO,
Flexible

Ligand

Docking
., J
Comput

Chem

21: 988
–
998, 2000.


P.
Nuno

Palma
,
Ludwig

Krippahl
, John E.
Wampler
,
and

Jose

J.G.
Moura
,
BiGGER
: A New (
Soft
)
Docking

Algorithm
., PROTEINS:
Structure
,
Function
,
and

Genetics

39:372
–
384 (2000).