Homology Modeling

Introduction (Sequence-Structure-Function
Relationships)
• Proteins of similar sequences fold into similar
structures and perform similar biological
functions.
• The protein sequence has the intrinsic
information to encode the protein structure.
 Introduction
• Structure-based drug design, analysis of
protein function, interactions, antigenic
behaviour, and rational design of proteins with
increased stability or novel functions.
• Many proteins are simply too large for NMR
analysis and cannot be crystallized for X-ray
diffraction.
 Structure Prediction from sequence

1.Homology (or comparative) modelling

2.Threading
3.Ab initio calculations

Homology modelling is most accurate and

powerful
 What is Homology Modeling?
• Homology modeling also known as comparative modeling
uses homologous sequences with known 3D structures
for the modelling and prediction of the structure of a
target sequence
• Homology modeling is one of the most best performing
prediction methods that gives “accurate” predicted
models.
 How does it work
• A homology modeling routine needs three items of input:
– The sequence of the protein with unknown 3D structure, the "target
sequence".
– A 3D template is chosen by virtue of having the highest sequence identity
with the target sequence. The 3D structure of the template must be
determined by reliable empirical methods such as crystallography or NMR,
and is typically a published atomic coordinate "PDB" file from the Protein
Data Bank.
– An alignment between the target sequence and the template sequence.
• First, the homology modeling routine arranges the backbone identically to that
of the template. This means that not only the positions of alpha carbons, but
also the phi and psi angles and secondary structure, are made identical to the
template. Next, the more sophisticated homology modeling packages adjust
side chain positions to minimize collisions, and may offer further energy
minimization or molecular dynamics in an attempt to improve the model.
 Steps of Homology Modeling
• It is a multi step process and almost all the steps
has to made.
1. Template Recognition and Initial Alignment
2. Alignment Correction
3. Backbone Generation
4. Loop Modeling
5. Side chain modeling
6. Model Optimization
7. Model Validation
 Available Software
• Insight [Dayringer, Tramontano, and Fletterick,
1986],
• Modeller [Sali and Blundell,1993],
• Swiss-Model [Peitsch, Schwede, and Guex, 2000],
• WHAT IF [Vriend, 1990]).
• Prime [Schrodinger Inc.]
• Phyre [Structural Bioinformatics Group, Imperial
College, London].
Template Recognition and Initial Alignment
 Template Recognition and Initial Alignment

• In the safe homology modelling zone the

percentage identity between the sequence of
interest and a possible template is high
enough to be detected with simple sequence
alignment programs such as BLAST (Altschul et
al., 1990) or FASTA (Pearson, 1990)
Alignment Correction
 Backbone Generation
When the alignment is ready, the actual model building can start.

If two aligned residues differ, only the backbone coordinates (N,Cα,C and O)
can be copied.
 Loop Modeling
• In the majority of cases, the alignment between
model and template sequence contains gaps.
• Either gaps in the model sequence (deletion) or in
the template sequence (insertions).
• In the first case, one simply omits residues from the
template, creating a hole in the model that must be
closed.
• In the second case, one takes the continuous
backbone from the template, cuts it, and inserts the
missing residues.
 Loop Modeling
• Knowledge based: one searches the PDB for
known loops with endpoints that match the
residues between which the loop has to be
inserted, and simply copies the loop conformation.
• Energy based: as in true ab initio fold prediction,
an energy function is used to judge the quality of a
loop. Then this function is minimized, using Monte
Carlo (Simons et al., 1999) or molecular dynamics
techniques
Quantitative comparison between model
and experimental 3D structure using
RMSD
• 0.0-0.5 Å • Essentially Identical
• <1.5 Å • Very good fit
• < 5.0 Å • Moderately good fit
• 5.0-7.0 Å • Structurally related
• > 7.0 Å • Dubious relationship
• > 12.0 Å • Completely unrelated
Taken from: http://redpoll.pharmacy.ualberta.ca/bioinfo301/Bioinf301-3Dvisualize.ppt
 BIOINFORMATICS PRACTICAL ON
HOMOLOGY MODLING
• Q. Perform a homology model of the given
protein sequence and generate the structure
of the structure in PDB format. The sequence
of the model is given below.

> protein
MPHKEKHPLQDMFTSAIEAVARDSGWAELSAVGSY
LAKNDPSFDPRNWGHGRLSQMVKKLDFLTVQESRN
GSKLHSEIRLRHDG
 Model Validation
• Various model validation parameters can be
considered such as RMSD , Ramachandran
Plot, Z-score value from ProSA-web server and
data from other server such as PROCHECK,
ERRAT and Verify3D programs, available at the
SAVES server.
• SUPERPOSE SERVER can be used for
calculation of RMSD value.