HOMOLOGY

MODELLING
Presentor:
Prof. Meet Desai
Dr. Tejas M. Dhameliya M. Pharm Sem I
En. No.
202280822003
Department of Pharmaceutical Chemistry &
Quality Assurance
L. M. College of Pharmacy (228)
Ahmedabad-380009
 INTRODUCTION OF HOMOLOGY
MODELLING
• Homology or comparative modeling uses
experimentally determined 3D structure of
another protein that has a similar amino acid
sequence.
• Homology modeling has become a useful tool for
the prediction of protein structure when only
sequence data are available.
• Structural information is often more valuable than
sequence alone for determining protein function.
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/homolo
gy-modeling
 • It is based on two major observations:
• (1) Structure of a protein is uniquely
determined by its amino acid sequence,
• (2) during evolution, the structure is more
conserved than the sequence such that similar
sequences adopt practically identical structure
and distantly related sequences show similarity
in folds.

https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/homolog
y-modeling
 INTRODUCTION TO PROTEIN
STRUCTURE
• Proteins are large, complex molecules exhibit a
remarkable versatility that allows them to
perform a myriad of activities that are
fundamental to life.
• A fundamental principle in all of protein science is
that protein structure leads to protein function.
• The distinctive structures of proteins allow for
the placement of particular chemical groups in
specific places in three-dimensional space.
Structural Bioinformatics, Methods of Biochemical Analysis, Philip E. Bourne Helge
Weissig, Eric D. Scheeff and J. Lynn Fink, Volume 44, Unit 2, pg no:- 16-17.
• Precise placement of chemical groups also allows
proteins to play important structural, transport,
regulatory functions and as a catalyst in organisms.

• Proteins are made up of small molecules known as

amino acids that consist of an alpha (central)
carbon atom linked to an amino group, a carboxyl
group, a hydrogen atom, and a variable component
called a side chain.
https://www.nature.com/scitable/topicpage/protein-structure-14122136/#:~:text=Protein
s%20are%20built%20from%20a,acids%20have%20nonpolar%20side%20chains
• Multiple amino acids are linked together by
peptide bonds, forming a long chain.
• The chemistry of amino acid side chains is
critical to protein structure because these side
chains can bond with one another to hold a
length of protein in a certain shape or
conformation.

https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/ho
mology-modeling
 HISTORY
•  The first homology modeling studies were done using
wire and plastic models of bonds and atoms as early
as the 1960’s.
• The models were constructed by taking the
coordinates of a known protein structure and
modified by hand for those amino acids that did not
match the structure.
• In 1969 David Phillips, Brown and co-workers
published the first paper regarding homology
modeling.
https://en.wikipedia.org/wiki/Homology_modeling
 STEPS OF HOMOLOGY MODELLING

• Homology modeling is a multistep method

involving the following steps:
• (1)Template recognition and initial alignment
• (2)Alignment correction
• (3)Backbone generation
• (4)Loop modeling
• (5)Side chain modeling

http://aidanbudd.github.io/ppisnd/trainingMaterial/allegraVia/PPI/tutorial_on_homolog
y_modelling.html
 (6)Model optimization
(7)Model validation (by hand or using different
servers)
(8)Iteration to correct mistakes (if any)

http://aidanbudd.github.io/ppisnd/trainingMaterial/allegraVia/PPI/tutorial_on_homology
_modelling.html
STEP 1: TEMPLATE RECOGNITION AND
INITIAL ALIGNMENT
• To identify the template, the program compares
the query sequence to all the sequences of
known structures in the PDB (e.g. BLAST)
• Usually, the template structure with the highest
sequence identity and coverage will be the first
option
• Other considerations:
• conformational state (i.e. active or inactive)

https://microbenotes.com/homology-modeling-working-steps-and-uses
• other molecules or multimeric complexes
• It is possible to choose multiple templates and
build multiple models.
• It is possible to combine multiple templates
into one structure that is used for modeling.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 2: ALIGNMENT CORRECTION
• Having identified one or more possible
modeling templates using the initial screen
described above, more sophisticated methods
are needed to arrive at a better alignment.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 3: BACKBONE GENERATION
• When the alignment is ready, the actual model building
can start.
• Creating the backbone is trivial for most of the model:
one simply transfers the coordinates of those template
residues that show up in the alignment with the model.
• If two aligned residues differ, the backbone coordinates
for N, α-C, C and O and often also the β-C can be copied.
• Conserved residues can be copied completely to provide
an initial guess.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 4: LOOP MODELING

• For the majority of homology model building

cases, the alignment between model and
template sequence contains gaps.
• Gaps in the model-sequence are addressed by
omitting residues from the template.
• Gaps in the template sequences are treated by
inserting missing residues into the continuous
backbone.

https://microbenotes.com/homology-modeling-working-steps-and-uses
• Changes in loop conformation are notoriously
hard to predict.
• Loop modeling: a search is made through the
PDB for known loops containing endpoints that
match the residues between which the loop is
to be inserted.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 5: SIDE CHAIN MODELING

• Libraries of common rotamers extracted from

high resolution X-ray structures are often used
to position side chains.
• The various rotamers are subsequently
explored and scored with a variety of energy
functions.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 6: MODEL OPTIMISATION

• To predict the side chain rotamers with high

accuracy, we need the correct backbone, which in
turn depends on the rotamers and their packing.
• The common approach to address this problem is
to iteratively model the rotamers and backbone
structure.
• First, we predict the rotamers, then remodel the
backbone to accommodate rotamers, followed by
a round of refitting the rotamers to the new
backbone.

https://microbenotes.com/homology-modeling-working-steps-and-uses
• This process is repeated until the solution
converges.
• This boils down to a series of rotamer
prediction and energy minimization steps.

https://microbenotes.com/homology-modeling-working-steps-and-uses
 STEP 7: MODEL VALIDATION

• Every protein structure contains errors, and

homology models are no exception.
• The number of errors (for a given method)
mainly depends on two values:
– The percentage sequence identity between
template and model-sequence
– The number of errors in the template

https://microbenotes.com/homology-modeling-working-steps-and-uses
• There are two principally different ways to
estimate errors in a structure
– Calculating the model’s energy based on a
force field.
– Determining normality indices that describe
how well a given characteristic of the model
resembles the same characteristic in real
structures.

https://microbenotes.com/homology-modeling-working-steps-and-uses
STEP 8: ITERATION TO CORRECT MISTAKES

• When errors in the model are recognized and

located, they can be corrected by iterating
portions of the homology modeling process.
• Small errors that are introduced during the
optimization step can be removed by running a
shorter molecular dynamics simulation.
• A error in a loop can be corrected by choosing
another loop conformation in the loop
modeling step.
https://microbenotes.com/homology-modeling-working-steps-and-uses
• Large mistakes in the backbone conformation
sometimes require the complete process to be
repeated with another alignment or even with
a different template.
• Valuable resources for homology modeling are
MODELLER and SWISS-MODEL.

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 USES OF HOMOLOGY MODELLING
• Protein modeling Provide a solid basis for:
• Rational design of proteins with increased stability or novel
functions.
• Analysis of protein function, interactions, antigenic
behavior.
• Structure-based drug design
• Because it is difficult and time-consuming to obtain
experimental structures from methods such as X-ray
crystallography and protein NMR for every protein of
interest, homology modeling can provide useful structural
models for generating hypotheses about a protein’s
function.
https://microbenotes.com/homology-modeling-working-steps-and-uses
 RECENT APPLICATIONS OF HOMOLOGY
MODELLING
• The Homology model of 17β-HSD2 (17β-
Hydroxysteroid dehydrogenase type 2) in complex
with NAD+ and 17β-estradiol was built, using a
multi-fragment "patchwork" approach.
• The molecular basis and the amino acids involved
in the enzymatic functionality are poorly
understood, as no crystal structure of the
membrane-associated 17β-HSD2 exists.
• The functional properties of only few amino acids
are known.
https://www.sciencedirect.com/science/article/abs/pii/S0960076020303150
• To determine the  17β-HSD2 topology and to
confirm the quality of the model, fifteen
selected amino acids were exchanged one by
one using site directed mutagenesis.
• The mutants’ functional behavior
demonstrated that the generated model was of
very good quality and allowed the identification
of several key amino acids involved in either
ligand or internal structure stabilization.

https://www.sciencedirect.com/science/article/abs/pii/S0960076020303150
 RECENT APPLICATIONS OF HOMOLOGY
MODELLING
• The Homology modeling of the  17β-HSD3
 membrane-associated enzyme was done to
check the 16-Picolyl-androsterone derivative
inhibitory activity towards the enzyme and
also to check the metabolic stability and
cytotoxic effect on various cancer cells.

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%20built%20from%20a,acids%20have%20nonpol
ar%20side%20chains
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THANK YOU