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7 HomologyModelling 12oct2020

The document discusses molecular modelling and drug design course content from the National Institute of Technology Durgapur. It lists reference books and sources for course slides. The content includes an overview of protein tertiary structure prediction methods, including homology modeling. Homology modeling predicts protein structures based on sequence homology to known structures. The process involves identifying a homologous template, aligning sequences, building a framework, adding side chains and loops, refinement, and model evaluation.

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22 views

7 HomologyModelling 12oct2020

The document discusses molecular modelling and drug design course content from the National Institute of Technology Durgapur. It lists reference books and sources for course slides. The content includes an overview of protein tertiary structure prediction methods, including homology modeling. Homology modeling predicts protein structures based on sequence homology to known structures. The process involves identifying a homologous template, aligning sequences, building a framework, adding side chains and loops, refinement, and model evaluation.

Uploaded by

things stranger
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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NATIONAL INSTITUTE OF TECHNOLOGY DURGAPUR

Course Name: Molecular Modelling and Drug Design


Course Code: BTE719
This presentation is solely meant for ACADEMIC PURPOSES and can be reused by others ONLY
for ACADEMIC USES with proper acknowledgments.
Reference Books:
1. Molecular Modelling And Drug Design By J.G. Vinter And Mark Gardner
2. Molecular Modelling: Principles And Applications By Andrew Leach
Some of the contents of the slides have been obtained from the following sites:
References:
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/homology-modeling
https://en.wikipedia.org/wiki/Homology_modeling#:~:text=Homology%20modeling%2C%20also%20known%20as,(the%20%22template%22).
https://swissmodel.expasy.org/

Name of the Faculty: Dr. Amita Barik


Department Name: Biotechnology
Computational Methods available for
structure prediction:
Protein Tertiary Structure Prediction

• One of the most important scientific achievements of the twentieth


century was the discovery of the DNA double helical structure by Watson
and Crick in 1953.

• Strictly speaking, the work was the result of a three-dimensional


modeling conducted partly based on data obtained from x-ray diffraction
of DNA and partly based on chemical bonding information established in
stereochemistry.

• It was clear at the time that the x-ray data obtained by their colleague
Rosalind Franklin were not sufficient to resolve the DNA structure.

• Watson and Crick conducted one of the first-known ab initio modeling of


a biological macromolecule, which has subsequently been proven to be
essentially correct.
CASP
• Many proteins are too large for NMR or lack the propensity to form diffraction quality crystals for X-
ray diffraction, so in such cases computational method for structure prediction is the only approach.

• Several algorithms to solve the problem -- each method has both advantages and disadvantages.

• Globally, a competition has been set up to evaluate the performance of several structure prediction
tools/softwares using blind test on several experimentally predetermined structures of proteins.

• This competition was started in 1995 as Critical Assessment of Techniques for Protein Structure
Prediction (CASP) which provides a global benchmark for this exhaustive computational purpose.
Structure Prediction

Template modelling
1. Homology modeling or comparative modeling
2. Threading or fold-recognition
(A) Homology Modeling

• Homology modeling predicts protein structures based on sequence


homology with known structures.

• It is based on the principle that similar sequences are likely to have


similar structures.

• For a given pair of highly similar protein sequences, if the structure of


first protein is known, then that can be used as a template to predict
the structure of second protein.
Flowchart -Homology Modeling
Steps in homology modelling
1. Identification of homologous sequence(s) in
the available protein structure databases
which can be used as template(s) for modeling
2. Alignment of the query/target and template
sequence(s)
3. Building a framework structure for the query
protein consisting of main chain atoms
4. Addition of side chain atoms and loops
5. Refinement and optimizing the entire model
based on energy criteria
6. Evaluation of the overall quality of the model
obtained.

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