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Knowledge-based scoring functions

Knowledge-based scoring functions are derived from a statistical analysis of structures of protein-ligand complexes in the RCSB Protein Databank (PDB). Searches are made for each possible pair of atoms in contact with each other. Interactions found to occur more frequently than would be predicted by random chance are considered attractive (stabilizing), and interactions that occur less frequently are considered repulsive (destabilizing). Examples of knowledge-based scoring functions include Muegge’s Potential of Mean Force function [3] and DrugScore [4] .

Rigid receptor docking

Parameterization of the problem

Many docking algorithms make the simplifying, but potentially quite inaccurate, assumption that the receptor is a rigid object and attempt to dock the ligand to it. The receptor conformation used is generally one from a receptor-ligand complex whose structure has been determined by x-ray crystallography or NMR spectroscopy. Because the receptor cannot move, the degrees of freedom of the problem are those of the ligand: three translational, three global-rotational, and one internal dihedral rotation for each rotatable bond. It is generally assumed that bond lengths and the angles formed by adjacent bonds do not change, and on the scale of most ligands (10 to 40 atoms), this assumption is a reasonable one. Docking to a rigid receptor is thus an optimization problem over a 6 + n dimensional space, where n is the number of rotatable bonds in the ligand.

Examples of rigid-receptor docking programs

Autodock 3.0

Autodock is actually a set of closely related programs and algorithms developed at the Scripps Research Institute and the University of California at San Diego.

Search technique

Autodock can use one of several optimization methods to search for the best placement of the ligand:

  • Simulated annealing: At each step of simulated annealing, the position and internal rotational state of the ligand is adjusted and the energy calculated. If the energy decreases, the move is accepted. If not, it may be accepted with some probability that depends on the current temperature of the annealing. As the search goes on, the temperature is decreased, and eventually, the final state of the ligand is returned as the docked conformation. Because simulated annealing is a Monte Carlo (randomized) method, different runs will generally produce different solutions.
  • A genetic algorithm: The genetic algorithm represents the states of the degrees of freedom of the ligand as a string of digits, and this string is referred to as a gene. A population of different genes is generated at random, and each is scored using the Autodock energy function. Genes are selected to form the next population based on their score, with better scoring genes more likely to be selected. A gene may be selected more than once, and some may not be selected at all. Pairs of the selected genes are allowed to cross over with each other. In this process, a segment of the gene is selected and the values in this range are exchanged between them. The hope is that by combined two partially good solutions, we will eventually find a better solution.
  • a Lamarckian genetic algorithm (LGA): This is the same as the standard genetic algorithm except that, before they are scored, each conformation (gene) is subjected to energy minimization. The next population is then founded by members of this energy-minimized population. The name "Lamarckian" refers to the failed genetic theory of Jean-Baptiste Lamarck, who held that an organism could pass on changed experienced in its lifetime to its offspring. This theory was eventually abandoned in favor of Mendel's now-familiar laws of inheritance. The LGA is faster than both simulated annealing and the standard genetic algorithm, and it allows the docking of ligands with more degrees of freedom.

Questions & Answers

How we are making nano material?
what is a peer
What is meant by 'nano scale'?
What is STMs full form?
scanning tunneling microscope
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
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
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
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.
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
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
characteristics of micro business
for teaching engĺish at school how nano technology help us
How can I make nanorobot?
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
how can I make nanorobot?
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
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.
what is the actual application of fullerenes nowadays?
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.
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.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
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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