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Amity Institute of Biotechnology

Docking of molecules involves finding the complementary binding pose between a target protein and ligand molecules. There are two main approaches: shape complementarity, which quickly scans ligands to see if they fit in the protein's active site, and simulation, which can better incorporate ligand flexibility. Popular docking programs include Hex, which performs molecular superposition, and FTDock, which implements a Fourier correlation algorithm for rigid-body docking predictions. Docking has applications in understanding cellular processes through protein-protein interactions, predicting ligand binding for drug design, and applications in bioremediation.

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107 views20 pages

Amity Institute of Biotechnology

Docking of molecules involves finding the complementary binding pose between a target protein and ligand molecules. There are two main approaches: shape complementarity, which quickly scans ligands to see if they fit in the protein's active site, and simulation, which can better incorporate ligand flexibility. Popular docking programs include Hex, which performs molecular superposition, and FTDock, which implements a Fourier correlation algorithm for rigid-body docking predictions. Docking has applications in understanding cellular processes through protein-protein interactions, predicting ligand binding for drug design, and applications in bioremediation.

Uploaded by

Sunny Kataria
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPT, PDF, TXT or read online on Scribd
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Amity Institute Of Biotechnology

Docking Of Molecules

By :
Shinoy Ali
Priyanka Jaiswal
B.Tech (Biotech)
Section - B
Definition of problem
Protein Small molecule Complex
Shape complementarity
It help to finding the complementary pose of
docking the target and the ligand molecules.
Fast and robust approach
It can quickly scan through several thousand
ligands in a matter of seconds.
It can figure out whether they can bind at the
protein’s active site.
Scalable to even protein-protein interactions.
Amenable to pharmacophore based approaches,
since they use geometric descriptions of the
ligands to find optimal binding.
Simulation
Advantages over Shape
complementarity
Simulation is more amenable to
incorporate ligand flexibility into its
modeling whereas shape complementarity
techniques have to use some ingenious
methods to incorporate flexibility in
ligands.
Hex
Hex is an interactive protein docking and
molecular superposition program.
Understands protein and DNA structures
in PDB format.
Hex will run on most Windows-XP,
Linux and Mac OS X PCs.
Latest version is 6.3.
FTDock
FTDock or Fourier Transform Dock
performs rigid-body docking on two
biomolecules in order to predict their
correct binding geometry.
It outputs multiple predictions that can be
screened using biochemical information.
FTDock implements the Fourier
correlation algorithm.
Protein- Protein docking
 Helps to determine molecular structure of
complexes.
 Understanding the cellular events.
Protein- Ligand docking
 To predict the position and orientation of
a ligand when bound to protein receptor.
 Protein receptor ligand can be:
 Rigid ligand with a flexible receptor
 Flexible ligand with a rigid receptor
Protein-DNA docking
 Proteins that bind DNA have common folding patterns
known as DNA binding motifs and domains. Recognition of
DNA by protein can take place at two levels: nonspecific
binding - between protein sidechains and DNA
sugar/phosphate backbone and specific binding - between
protein sidechains and nucleotide bases.
Applications
LIGAND BASED
STRUCTURE BASED
Other Applications:-
Bioremediation – Protein ligand docking
can also be used to predict pollutants that
can be degraded by enzymes.
Predicting the molecule complex.
Hit identification.

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