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Scoring function

FlexX uses a variant of the SCORE1 scoring function developed by Hans-Joachim Boehm for the de novo enzyme inhibitor design package LUDI. The scoring function has the following form:

Where f is a penalty function for deviations from ideal geometry for each kind of interaction, and f* is a function penalizing for lipophilic interactions deviating from an ideal separation distance.

Dock

Dock 1.0, first described in 1982 [8] , was the first automated receptor-ligand docking program. It was developed in the Department of Pharmacology at the University of California at San Francisco. Dock 4.0, the current version, was released in 1997 [9] .

Search technique

Like FlexX, Dock is driven by the geometry of the ligand and active site. The program approximates the shape of the binding cavity of the receptor with spheres. It then attempts to match the ligand to some subset of the centers of these spheres. Early versions used geometric hashing (see this module, covering local alignment methods ) to perform this matching, but more recent versions use bipartite graph matching (version 3.5) and single graph matching (version 4.0) for improved speed.

Scoring function

Dock offers three scoring functions. The first is based on an approximation to the Lennard-Jones potential (Van der Waals interactions). This essentially enforces geometric alignment and shape constraints. The second uses the program DELPHI to calculate the electrostatic potential of the complex.The third calculates the energy of the complex under the AMBER force field.

Flexible receptor docking

Introduction

As previously mentioned, docking entails determining not only the identity and three dimensional structure of the bound ligand, but also how the binding process affects the conformation of the receptor. This section will review the different receptor flexibility representations that have been proposed to study receptor conformational changes in the context of structure based drug design.

A central paradigm which was used in the development of the first docking programs was the lock-and-key model first described by Fischer [10] . In this model the three dimensional structure of the ligand and the receptor complement each other in the same way that a lock complements a key. However, further work confirmed that the lock-and-key model is not the most correct description for ligand binding. A more accurate view of this process was first presented by Koshland [11] in the induced fit model. In this model the three dimensional structure of the ligand and the receptor adapt to each other during the binding process. It is important to note that not only the structure of the ligand but also the structure of the receptor changes during the binding process. This occurs because the introduction of a ligand modifies the chemical and structural environment of the receptor. As a result, the unbound protein conformational substates, corresponding to the low energy regions of the protein energy landscape are likely to change. The induced fit model is supported by multiple observations in different proteins such as streptavidin, HIV-1 protease, DHFR, aldose reductase and many others.

Questions & Answers

what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
Daniel
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
Maciej
characteristics of micro business
Abigail
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Anassong
Do somebody tell me a best nano engineering book for beginners?
s. Reply
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
s.
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
Tarell
what is the actual application of fullerenes nowadays?
Damian
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
Tarell
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
Virgil
is Bucky paper clear?
CYNTHIA
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Harper
Do you know which machine is used to that process?
s.
how to fabricate graphene ink ?
SUYASH Reply
for screen printed electrodes ?
SUYASH
What is lattice structure?
s. Reply
of graphene you mean?
Ebrahim
or in general
Ebrahim
in general
s.
Graphene has a hexagonal structure
tahir
On having this app for quite a bit time, Haven't realised there's a chat room in it.
Cied
what is biological synthesis of nanoparticles
Sanket Reply
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
China
Cied
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
Porter
many many of nanotubes
Porter
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Yasmin
what is the function of carbon nanotubes?
Cesar
I'm interested in nanotube
Uday
what is nanomaterials​ and their applications of sensors.
Ramkumar Reply
what is nano technology
Sravani Reply
what is system testing?
AMJAD
preparation of nanomaterial
Victor Reply
how to synthesize TiO2 nanoparticles by chemical methods
Zubear
what's the program
Jordan
?
Jordan
what chemical
Jordan
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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