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Docking

The document discusses docking techniques which attempt to predict the preferred orientation of one molecule binding to another. It defines docking, describes manual and molecular docking approaches, and covers topics like rigid and flexible docking between proteins, ligands, and other molecules. It also discusses recent advances and future directions of docking as well as common docking software and limitations.

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37 views13 pages

Docking

The document discusses docking techniques which attempt to predict the preferred orientation of one molecule binding to another. It defines docking, describes manual and molecular docking approaches, and covers topics like rigid and flexible docking between proteins, ligands, and other molecules. It also discusses recent advances and future directions of docking as well as common docking software and limitations.

Uploaded by

09sangeetachaudhary
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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Docking Technique

Introduction

Docking is an attempt to find the best matching between two molecules. • A


more serious definition…. • Docking is a method which predicts the preferred
orientation of one ligand when bound in an active site to form a stable
complex. • Finding the correct relative orientation of the “key” which will
open up the “lock”. • The protein can be thought of as the “lock” and the
ligand can be thought of as a “key”.
Introduction

1. Successful docking
methods search high-
dimensional spaces
effectively and use a
scoring function that
correctly ranks candidate
dockings
Manual Docking
Dock or fit a molecule in the binding site Binding group on the ligand and binding
site are known, defined by the operator. Ideal bonding distance for potential
interaction is defined. Binding group in the ligand is paired with its complementary
group in the binding site Docking procedure is started The program try to get best
fit, as defined by the operator. The paired groups are not directly overlaid, they are
fitted within preferred bonding distance. Both ligand and protein remain same
conformation throughout the process Same as in energy minimization. So this is a
rigid fit, once a molecule successfully docked fit optimization is carried out.
Different conformation of molecule can be docked to in same way Identify the best
fit
Molecular Docking

Molecular docking Identification of correct ligand binding Prediction of


binding affinity Rational Drug Design.

Molecular Docking- the process by which molecular modeling software fits a


molecule into target binding sites.

• Used for finding binding modes of protein with ligands/inhibitors.

• In molecular docking, attempt to predict the structure of the intermolecular


complex formed between two or more molecules.
Types of docking

Rigid Docking (Lock and Key) In rigid docking, the internal geometry of both
the receptor and ligand are treated as rigid.

Flexible Docking (Induced fit) An enumeration on the rotations of one of the


molecules (usually smaller one) is performed. Every rotation the energy is
calculated; later the most optimum pose is selected.
Docking can be between…

. • Protein – Ligand

• Protein – Protein

• Protein – Nucleotide
Recent advancement in Docking

The recent advances in Docking development of new scoring function that better capture
the entropic effect of ligand binding. Incorporation of explicit solvent molecule in
docking simulation in account to solvation effect , and use of machine learning algorithm
to improve the accuracy of binding affinity prediction.

Other developments like fragment based docking approaches which breakdown larger
molecule into smaller fragment that can docked individually and then reassembled.
Requirement
Protein (Enzyme, peptide)

• Ligand (Drug, novel compound, testing


compound, organic compound.

Docking Software (Autodock)

• Result analysis
Future directional of docking

It include the more accurate scoring function that take into account the nature
of ligand - protein interactions , the incorporation of protein flexibility in
docking stimulation to better model induce fit and conformational changes
and use of better hybrid methods that combine docking with other
computional and experimental things.Other areas of research that include the
algorithm and new software tools that docking stimulation faster and more
efficient , exploration of new type of molecules beyond traditional drug like
compound .
Docking software

SANJEEVINI – IIT Delhi

GOLD – University of Cambridge ,UK

AUTODOCK - Scripps Research Institute,USA

GemDock(Generic Evolutionary Method for Molecular Docking) A tool,


developed by Jinn-Moon Yang, a professor of the Institute of Bioinformatics,
National Chiao Tung University, Taiwan

Hex Protein Docking - University of Aberdeen, UK

GRAMM (Global Range Molecular Matching) Protein docking - A Center for


Bioinformatics, University of Kansas, USA Docking Software
Limitations

The major limitation in virtual screening by pharmacophore is the absence of good


scoring metrics.

• Whereas docking simulations are based on scoring functions trying to predict the
affinity, and similarity searches utilize similarity metrics.

• Pharmacophore queries do not have a reliable, general scoring metric.

•Most commonly, the quality of fitting the ligand into a pharmacophore query is
expressed by the root mean square deviation between the features of the query and
atoms of the molecule.
Thank-you

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