1.
PROTEIN STRUCTURE PREDICTION
Presented by – Siddika Arif Attar
M.SC BIOTECHNOLOGY

2.
 Introduction
 Methods for protein structure prediction
 Basic concept
 Homology modeling
 Folding recognition
 Ab –intio method
INDEX

3.
Introduction :
protein structure prediction-
protein structure prediction is the inference of the 3-D structure of protein
From its amino acid.
i.e. The predicton of its secondory & tertiory structure from primary structure.

4.
Methods for protein structure prediction
1. Experimental method 2. Computational method
 X-Ray Crystallography
 NMR Spectroscopy
 Electron Microscopy
 Homology modeling
 Fold Recognition
 Ab – Intio method

5.
Basic concept

6.
1. Homology modeling
 Knowledge based modeling.
 Based on sequence similarity with a protein.
 For which a structure has been predicted .

7.
Steps in homology modeling
1. Target recognition :
 Search related protein sequence in any strucrural database.
 FASTA &BLAST from EMBL-EBI & NCBI can be used ‘
2. Template selection :
 Slection on the basis of higher similarity ,close- subfamily phylogenetic tree & purpose
of modeling
3. Alignment sequence :
 The sequence similarity is too high then global alignment used.
 The best alignment methods are Cludtal X ,MUSCLE, T-Coffe & MAFFT .

8.
4. Model Building :
 Use MODELLER of model building i.e. Max Mod , PY Mod , PRIMO.
5. Model Evaluation :
 Accuracy of the model depend upon its sequence identity with the template.
Fig .Homology Modeling

9.
2. Folding recognition
Two Algorithms :
 Pairwise energy based method [ threading]
 Profile based method [fold recognition]
1. Pairwise energy based method :
 Searach for structural fold database by using energy based criteria.
 Using a dynamic programming & heuristic approaches .
 Calculate energy for raw model .
 Lowest energy fold is the best model .

10.
2. Profile based method
 A profile is constructed for related protein structure
 Generated by superimposition if structures to expose corresponding residues.
 Similarity depend upon the secondary structure ,polarity, hydrophobicity.

11.
3. Ab – Intio Method
 Ab – Intio method predict the proteins structure based on the physical methods .
 These method build protein 3-D structures .
 In Ab – Intio method ,Rosetta tool can be used .
Rosetta
 Breaks down the query sequence into many short segments
 Predict the secondary structure of small segments using HMMSTR.
 Segments with assigned secondary structure & assembled into 3D configuration.
 A large number of models are build & their over all energy potential calculated .
 Conformation with lowest energy is choosen as the best model.

12.
THANK YOU !