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Tertiary Protein Structure

Alignment

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Agenda Introduction

Mohammed El-shemy

PDBs. and ROSS

Mohammed Abbass

Comparison Stage in ROSS

Shukri Saleh

System Architecture

Abdalla Abbass

System Implementation and Conclusion

Ahmed Ali

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Introduction

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Bioinformatics

Using computer science in collecting and analyzing cbiological data .

genetic codes

Bioinformatics problems

DNA mapping

protein structure prediction and structure alignment

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Protein Structure Alignment

Structure

Amino Acid

Nucleotide

Levels

First Secondary

Tertiary

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PDBs. and ROSS

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PDB Structure Helix & Sheet

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PDB Structure Atom

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What is Inter-direction ?

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ROSS

Preprocessing

Initial Alignment

Final Alignment

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Preprocessing Flowchart

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Descriptor File Format

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Comparison Stage in

ROSS

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Initial Alignment

Query protein rotation

Calculating Score matrix

Finding best score matrix

Calculating SSEs matches

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Initial Alignment Cont.

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Final Alignment

Calculating initial distance d0

0 1.24 min 1, 2 1.0 15,

3 1.

Applying Kabsch for SSEs matched at initial alignme

Calculating new distance for pairs of atoms di

Applying Kabsch algorithm

Measuring distance gap using TM score.

+(

. . )

=

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Final Alignment Cont.

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System Architecture

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Development environment

Its java web application.

Why ? To target more audience over internet.

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System packages

Model

Preprocessing Alignment

Servlet Controller

DBC

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Class Diagram

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ERD

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SystemImplementation

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Used libraries

Jmol library

Open source molecule viewer.

View 3D chemical structure with features for chemicals

and bio molecules.

JmolApplet and JmolViewer.

JFreeChart Library

iText Library

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Proposed Solution

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Proposed Solution Cont.

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Conclusion

ROSS

ROSS algorithm emulates to be one of the most algorithspeed of processing and storage saving compared to othimplementation became more needy to researchers andusers

Availability at anytime and anywhere

Comparing with another algorithms ex.

TM-Align , VAST ,and SSM

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Future Work

Prediction

if there is a data loss in the alignment stage of one proteneed to predicate the second one

Caching process in the database

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References

1. Dr. Ahmed Seif Allah Ahmed Fadel, A Hierarchical Data Reduction Approach for

Structural Alignment of Proteins.Helwan University, PHD Thesis 2013.

2. jmol.sourceforge.net/

3. wiki.jmol.org/

4. www.rcsb.org/

5. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html

6. http://www.jfree.org/jfreechart/

7. http://itextpdf.com/

8. http://java-source.net/open-source/pdf-libraries/itext

9. http://zhanglab.ccmb.med.umich.edu/TM-score/

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Questions?

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Thank You!