Principle Investigator


Educational background :

2010: Ph.D. of Bioinformatics at University of Tehran

Thesis: “Prediction of protein backbone based on local fragment minimum energy”.

2000: Master of Science in Biophysics (Tarbiat-Modarres University)

Thesis: “Prediction of Protein Surface Accessibility using Information Theory”.

1997: Bachelor of Science in Microbiology (University of Tehran).


Relevant Experiences:

1.Organization: Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University

Location: Tehran

Date Worked: 2010 – up to now

Position Title: Head of Biophysics Department

2. Organization: Institute for Studies in Theoretical Physics and Mathematics (IPM)

 Location: Tehran

Date Worked: Oct 2004 – up to now

Position Title: Linux Server Administrator (Bioinformatics Group)

3.Organization: National Institute of Genetic Engineering & Biotechnology (NIGEB)

Location: Tehran

Date Worked: May 2003 – Oct 2005

Position Title: Software Team Manager

4.Organization: ARA System Consultant (Private Co.)

Location: Tehran

Date Worked: May 2000 – Oct 2002

Position Title: Software Team Manager

5.Organization: Tarbiat Modares University

Location: Tehran

Dates Worked: Oct 1997 – May 2000

Position Title: Administrator of Macromolecular Modeling Center of TMU

Honors and Awards:

2004 : Ranked First in Ph.D. Entrance Exam (Tehran University)

2000 : Distinguished researcher in Tarbiat Modares University


Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang and David van der Spoel (2013) MemBuilder: A Web-Based Graphical Interface to Build Heterogeneously Mixed Membrane Bilayers for the GROMACS Biomolecular Simulation Program. Bioinformatics, [First published online: November 22, 2013]  doi: 10.1093/bioinformatics/btt680

Nazanin Pirooznia, Sadegh Hasannia, Seyed Shahriar Arab, Abbas Sahebghadam Lotfi and Mostafa Ghanei (2013) The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases. Theoretical Biology and Medical Modelling, 10,13 doi:10.1186/1742-4682-10-36

Behnam Neyshabur, Ahmadreza Khadem, Somaye Hashemifar, Seyed Shahriar Arab (2013) NETAL: A new graph-based method for global alignment of protein-protein interaction networks. Bioinformatics 1:9. doi: 10.1093/bioinformatics/btt202

Seyed Shahriar Arab, Mohammadbagher Parsa Gharamaleki, Zaiddodine Pashandi, Rezvan Mobasseri (2013) Putracer: A Novel Method For Identification Of Continuous-Domains In Multi-Domain Proteins. Journal of Bioinformatics and Computational Biology. Vol. 11, No. 1  doi: 10.1142/S021972001340012X

Ayati M, Taheri G, Arab S, Wong L, Eslahchi C (2010) Overcoming Drug Resistance by Co-Targeting. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 198–201, Hong Kong.

Arab S, Sadeghi M, Eslahchi C, Pezeshk H. A  (2010) A pairwise residue contact area-based mean force potential for discrimination of native protein structure. BMC Bioinformatics, 11:16  doi:10.1186/1471-2105-11-16 .

Eslahchi C., Pezeshk H., Sadeghi M., Rahimi A. M., Maboudi Afkham H., Arab S (2009) Ston: A Novel Method for Protein three-dimensional Structure Comparison. Computers in Biology and Medicine, 39, 2: 166-172. doi: 10.1016/j.compbiomed.2008.12.004

Sheari A, Kargar M, Katanforoush A, Arab S, Sadeghi M, Pezeshk H, Eslahchi C, Marashi S.A. (2008)   A Tale of two Symmetrical Tails: Structural and Functional Charateristics of Palindroms in Proteins. BMC Bioinformatics, 9:274. doi:  10.1186/1471-2105-9-274

Shahriar Arab, Farzad Didehvar, Changiz Eslahchi, Mehdi Sadeghi (2007) Helix segment assignment in proteins using fuzzy logic. IRANIAN JOURNAL of BIOTECHNOLOGY, Vol. 5, 93-99

Roghayeh Zarei, Shahriar Arab and Mehdi Sadeghi (2007) A Method for Protein Accessibility Prediction based on Residue Types and Conformational States. Computational Biology and Chemistry, Vol. 31, 384–388 doi: 10.1016/j.compbiolchem.2007.08.006

Mehdi Sadeghi, Sahar Parto, Shahriar Arab, Bijan Ranjbar. (2005) Prediction of Protein Secondary Structure Based on Residue Pair types and Conformational States using Dynamic Programming Algorithm. FEBS Letters 579,  3397–3400

Hossein Naderi-Manesh, Mehdi Sadeghi, Shahriar Arab, and Ali A.Moosavi Movahed. (2001) Prediction of Protein Surface Accessibility with Information Theory. PROTEINS: Structure, Function, and Genetics 42: 452 – 459



  1. Seyed Shahriar Arab, Niloofar Shirvanizadeh. LinDA ,Linker Design Assistant:A new server for designing linkers in fusion protein.  13th Iranian congress of Biochemistry & 5th International Congress of Biochemistry and Molecular Biology & 1th Symposium on Metabolic Discovers, Yazd, IRAN April 15-18, 2013
  2. Seyed Shahriar Arab, Niloofar Shirvanizadeh. A database for peptide fragments: A new perspective to designing fusion proteins. The 4th Iranian conference on bioinformatics, National Institute for Genetic Engineering and Biotechnology, IRAN November 6-7, 2012
  3. Seyed Shahriar Arab, Mohammadbagher Parsa Gharamaleki, Zaiddodine Pashandi, Rezvan Mobasseri. Putracer: A Novel Method For Identification Of Continuous-Domains In Multi-Domain Proteins. The 8th International Conference on Bioinformatics of Genome Regulation and Structure\Systems Biology, Novosibirsk, RUSSIA June 25-29,2012
  4. S. Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk. A Trusty Knowledge-Based Potential Energy Based on Pairwise Residue Contact Area.ECCB08, European Conference on Computational Biology, September 22nd – 26th2008, Cagliari, Sardinia-Italy
  5. Armita Sheari, S. Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi. Prediction of Protein Flexible/Rigid Regions Based on Sequence.ECCB08, European Conference on Computational Biology, September 22nd – 26th2008, Cagliari, Sardinia-Italy
  6. S. Arab, Ch. Eslahchi, M. Sadeghi, H. Pezeshk, A. M. Rahimi, H. Maboudi Afkham. STON: A novel method for protein three dimensional structure comparison. The 5th National Biotechnology Congress of Iran. 24-26 Nov. 2007, Summit Meeting Conference Hall, Tehran-Iran
  7. M. Sadeghi, S. Arab, Ch. Eslahchi, F. Didehvar.  Fuzzy Secondary Structures. Mathematics conference. Jan, 2005, University of Ahvaz,  IRAN
  8. M. Sadeghi, S. Arab. Back translation of protein sequences using information theory.  1st Iranian Bioinformatics conference.  September 3, 2003, University of Tehran, IBB, IRAN
  9. D. Ajloo, M. Sadeghi, S. Arab, H. Naderi-Manesh, A. A. Saboury and A. A. Moosavi-Movahedi. The comparative stability and accessible surface area of avian and vertebrate hemoglobins. 15th FAOBMB Symposium – Perspectives of Biochemistry and Molecular Biology in 21 Century. October 21-24, 2000, Beijing, China
  10. M. Sadeghi, H. Naderi-Manesh, S. Arab and A. A. Moosavi-Movahedi. Prediction of amino acid surface accessibility and intermediate in prediction of protein structure. 4th Iranian Biophysical chemistry seminar. February 15-17, 2000 Institute of biochemistry & Biophysics, university of Tehran
  11. Hossein Naderi-Manesh, Yazdani, and Shahriar Arab. Stability and structure of some modified proteins. 8th international symposium protein structure & function relationship.  5-7 February 1999, Karachi, Pakistan
  12. Hossein Naderi-Manesh, Mehdi Sadeghi, Shahriar Arab, and Ali A.Moosavi Movahedi. Prediction of accessibility surface area in protein by a neural network system. Third European Symposium of the Protein Society.  September 19-22 September 1999– Garmisch-Partenkirchen, Germany
  13. Hossein Naderi-Manesh, Mehdi Sadeghi, Shahriar Arab, and Ali A.Moosavi Movahedi. Prediction of Surface and secondary elements base on hydrophaty scale. 37th IUPAC Congress, Frontiers in chemistry: Molecular Basis of Life. Sciences, Berlin, Germany.  August 14- 19, 1999
  14. Hossein Naderi-Manesh, Mehdi Sadeghi, and Shahriar Arab. Prediction of interior and solvent accessible segments of proteins. The Seventh Iranian Biology Conference.  2-24 AUG 1998, Isfahan – IRAN.

Current Projects:

– Protein secondary structure assignment using fuzzy logic

Under review. Web based interface is developed and it’s available (FAssign)

-Prediction of Protein’s Active Site

(S. Arab*, M.A. Abasi Dezfuli, N. Hoseini Manesh)

 -Mean Scaled RMSD: A Size independent Measure for Superimposition of Protein Structures

-PredEval: How much a prediction method is good

 -FoldSim: Protein Folding Simulator


Tarbiat Modares University, 2010 -now

IPM Bioinformatics, 2004-now

Iranian Bioinformatics Society, 2005

National Institute of Genetic Engineering & Biotechnology (NIGEB) 2003

Iranian Biophysical chemistry Society, 2000

Iranian Biological Society, 1997

Skills in computer science:


C++, Visual Basic, Perl, Matlab, Familiar with R


VB Script,  Microsoft Visual InterDev, Front Page


Microsoft SQL Serve, MySQL


Mac OS X, Windows, LINUX, IRIX


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