Tertiary Protein Structure

Alignment
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
Introduction
Bioinformatics
• Using computer science in collecting and analyzing complex
biological data .

• genetic codes

• Bioinformatics problems

• DNA mapping
• protein structure prediction and structure alignment

Protein Structure Alignment

• Structure

• Amino Acid
• Nucleotide

• Levels
• First
• Secondary
• Tertiary

PDBs. and ROSS
PDB Structure – Helix & Sheet

PDB Structure – Atom

What is Inter-direction ?

ROSS
• Preprocessing

• Initial Alignment

• Final Alignment

Preprocessing Flowchart
Descriptor File Format
Comparison Stage in
ROSS
Initial Alignment
• Query protein rotation
• Calculating Score matrix
• Finding best score matrix
• Calculating SSEs matches


Initial Alignment Cont.
Final Alignment
• Calculating initial distance d
0
• 0 = 1.24 ∗ min 1, 2 ∗ 1.0 − 15,
1
3
− 1.8
• Applying Kabsch for SSEs matched at initial alignment
• Calculating new distance for pairs of atoms d
i
• Applying Kabsch algorithm
• Measuring distance gap using TM score.
• =
1

1
1+(

1.24 −15−1.8
3
)
2

=1


Final Alignment Cont.
System Architecture
Development environment
• It’s java web application.

• Why ?
• To target more audience over internet.
System packages
• Model
• Preprocessing
• Alignment
• Servlet Controller
• DBC

Class Diagram
ERD
System
Implementation
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

Proposed Solution
Proposed Solution Cont.
Conclusion
• ROSS

• ROSS algorithm emulates to be one of the most algorithms using by its
speed of processing and storage saving compared to others, and its
implementation became more needy to researchers and Bioinformatics
users

• Availability at anytime and anywhere

• Comparing with another algorithms ex.
• TM-Align , VAST ,and SSM

Future Work
• Prediction

• if there is a data loss in the alignment stage of one protein to another, we
need to predicate the second one

• Caching process in the database

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/
Questions?
Thank You!

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