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Formally, the protein-ligand docking problem is the following: We are given a geometric and chemical description of a protein and an arbitrary small organic molecule. We want to determine computationally whether the small molecule will bind to the protein, and if so, we would like to estimate the geometry of the bound complex, as well as the affinity of the binding. Most algorithms include two components: a search technique to find the optimal placement of the ligand in the binding pocket of the protein, and a scoring function to rate each placement, as well as to rank candidate ligands against each other. The remainder of this module will cover a range of docking approaches, starting with the simplest, rigid-receptor methods, which make very restrictive assumptions about the dynamics of the protein and candidate ligands, and then moving on to more complex approaches that allow the receptor to change conformation. The latter methods have the potential to identify ligands that might be missed by simpler approaches.

Trypsin, a protease involved in digestion (PDB structure ID 3ptb)
Benzamidine, a trypsin inhibitor (PDB structure ID 3ptb)
Stereo view of benzamidine (red) docked in the active site of trypsin (blue) (PDB structure ID 3ptb)

Components of a docking program

As stated earlier, protein-ligand docking methods generally consist of two components: a ligand placement algorithm to enumerate and test possible poses for the ligand in the protein's active site, and a scoring function to evaluate each placement, as well as to evaluate one candidate ligand against another. Each of these componets is introduced in more detail below.

Ligand placement algorithm

The first part of any docking technique is a method to place the ligand in various candidate poses in the binding pocket of the receptor. Although each placement could be completely random and independent, most algorithms either use heuristics based on the chemistry or geometry of the atoms involved (FlexX, DOCK), or use a standard optimization technique such as simulated annealing or a genetic algorithm (Autodock, Gold). A few use explicit molecular dynamics simulation.

Scoring function

The scoring function provides a way to rank placements of ligands relative to one another. Ideally, the score should correspond directly to the binding affinity of the ligand for the protein, so that the best scoring ligands are the best binders. Scoring functions generally fall into three categories:

Explicit force field scoring function

Modified versions of both the AMBER and CHARMM force fields (see this module for more on force fields) have been used as scoring functions. For some complexes, they have been found to provide a good approximation of the free energy of binding. Early versions of Autodock used a subset of the AMBER force field.

Empirical scoring functions

The score is expressed as a weighted sum: i i interactions ΔG i f i l, r where ΔG i is an empirically determined weight for the ith interaction type. It corresponds to the average free energy contribution of a single interaction of that type over the set of receptor-ligand systems used to normalize the scoring function. The types of interactions that might be included in an empirical scoring function include hydrogen bonds, electrostatic interactions, hydrophobic contacts, solvent exclusion volume, and electrostatic interactions, among others. Examples of empirical scoring functions include the Autodock 3.0 scoring function (see below), Protherics Inc.’s ChemScore [1] , and Boehm’s SCORE1 [2] .

Questions & Answers

Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
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
hi
Loga
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
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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