The document provides an overview of protein structure prediction methods, including homology modeling, folding recognition, and ab-initio methods. It outlines the steps involved in homology modeling such as target recognition, template selection, sequence alignment, model building, and evaluation. Additionally, it discusses algorithms for folding recognition based on energy and profile methods, and the use of the Rosetta tool in ab-initio structure prediction.

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 !