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More information about some of these proteins and other proteins motions can be found at the following links:

Although it has been clearly established that a protein is able to undergo conformational changes during the binding process, most docking studies consider the protein as a rigid structure. The reason for this crude approximation is the extraordinary increase in computational complexity that is required to include the degrees of freedom of a protein in a modeling study. There is currently no computationally efficient docking method that is able to screen a large database of potential ligands against a target receptor while considering the full flexibility of both ligand and receptor. In order for this process to become efficient, it is necessary to find a representation for protein flexibility that avoids the direct search of a solution space comprised of thousands of degrees of freedom. What follows is a brief review of the different representations that have been used to incorporate protein flexibility in the modeling of protein/ligand interactions. A common theme behind all these approaches is that the accuracy of the results is usually directly proportional to the computational complexity of the representation. The different types of flexibility representations models are grouped into categories that illustrate some of the key ideas that have been presented in the literature in recent years. However it is important to note that the boundaries between these categories are not rigid and in fact several of the publications referenced below could easily fall in more than one category.

Flexibility representations

Soft receptors

Perhaps the simplest solution to represent some degree of receptor flexibility in docking applications is the use of soft receptors. Soft receptors can be easily generated by relaxing the high energy penalty that the system incurs when an atom in the ligand overlaps an atom in the receptor structure. By reducing the van der Waals contributions to the total energy score the receptor is in practice made softer, thus allowing, for example, a larger ligand to fit in a binding site determined experimentally for a smaller molecule (see Figure 6). The rationale behind this approach is that the receptor structure has some inherent flexibility which allows it to adapt to slightly differently shaped ligands by resorting to small variations in the orientation of binding site chains and backbone positions. If the change in the receptor conformation is small enough, it is assumed that the receptor is capable of such a conformational change, given its large number of degrees of freedom, even though the conformational change itself is not modeled explicitly. It is also assumed that the change in protein conformation does not incur a sufficiently high energetic penalty to offset the improved interaction energy between the ligand and the receptor. The main advantage of using soft receptors is ease of implementation (docking algorithms stay unchanged) and speed (the cost of evaluating the scoring function is the same as for the rigid case).

a) Three dimensional van der Walls representation of a target receptor. b) Close up image of a section of the binding site. For the purposes of rigid protein docking, the receptor is commonly described by the union of the volumes occupied by its atoms. The steric collision of any atom of the candidate ligand with the atoms of the receptor will result in a high energetic penalty. c) Same section of the binding site as shown in b) but with reduced radii for the atoms in the receptor. This type of soft representation allows ligand atoms to enter the shaded area without incurring a high energetic penalty.

Questions & Answers

Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
research.net
kanaga
sciencedirect big data base
Ernesto
Introduction about quantum dots in nanotechnology
Praveena Reply
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
for teaching engĺish at school how nano technology help us
Anassong
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
NANO
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
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
NANO
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
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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