Molecular dynamics
Molecular dynamics is a
computer simulation technique to observe the movement of molecules interacting.
This technique simulates molecules attract each other and pushing and bumping
into each other. Molecular dynamics simulations provide static and dynamic
information on the atomic scale, such as position and velocity. This
information can then be processed into information on a macroscopic scale such
as pressure, temperature and others.
Molecular dynamics
method is a simulation method that is very useful in studying molecular systems
such as organic molecules in solution and macromolecular compounds in the
metabolic process. This method allows the depiction of the structure,
thermodynamic properties, and the dynamic nature of the system in the condensed
phase. The principal part of the simulation methodology is the availability of
potential energy function is accurate to model the properties of the system
under study. The potential energy function can be arranged through the method
of quantum mechanics or molecular mechanics. The problem that arises is QM can
only be used for simple systems with a few tens of units of mass -mengingat
that QM calculations require long- time while the MM method is not sufficiently
thorough. To overcome this problem, developed a method known as hybridization
QM / MM, which is an important part of the system under study is calculated by
the method of QM, while the system does not have to be explained in detail
calculated by the method of MM. Method QM / MM simulations are widely used in
catalytic enzymatic reactions, chemical processes in solution and in the
receptor protein dockingsuatu.
Docking
Docking is a method for
predicting the preferred orientation of a molecule when bound to one another to
form a stable complex. Oreintasi information about this can be used to predict
the strength of the relationship or affinity between two molecules are used.
The relationship between the relevant biological molecules such as proteins,
nucleic acids, carbohydrates, and lipids have an important role in signal
transduction. Furthermore, the relative orientation of the two interacting
pairs can influence the type of signal that is generated.
Docking done to
computationally simulate the molecular recognition process. The purpose of
docking is to achieve the conformation of the protein and ligand are optimized
so that the free energy of the system as a whole is minimized. Docking help in
studying drug / ligand or receptor interactions / active protein by identifying
suitable sites on the protein, get the best geometry of the ligand-receptor
complex, and calculate the energy of the interaction of different ligands to
design a more effective ligand.
In order to perform the
docking, the first requirement is the structure of protein and ligand as desired.
Usually the structure has been determined using biophysical techniques such as
x-ray crystallography or NMR spectroscopy, is then stored in the Protein Data
Bank. As for the ligand to be used can be made with a chemical drawing software
like ChemDraw or Marvinsketch. Protein structure and potential ligands database
serves as input for docking program.
Docking program
consists of two parts, the docking algorithms / docking poses and scoring
function. Docking algorithms / pose works to find the orientation /
conformation of a ligand to its receptor mooring sites in order to get the most
stable conformation of a ligand-protein complex formed. Group - a functional
group ligand will interact with residue - receptor protein amino acid residues
to form intermolecular bonds. The strength of this bond were calculated and
stratified (ranking) with Scoring function.
Scoring function serves
to calculate affinity ligand-protein receptor complex is formed. This
identification is based on several theories such as the theory of Gibbs free
energy (ΔGbind). Gibbs free energy value is small shows that the conformation
that is formed is stable, while the value of the Gibbs free energy of the shows
less stable complexes formed. The more negative the value is generated, the
better affinity ligand-protein complex, so expect even more good activities.
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