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Dr. Parthiban Marimuthu, Ph.D.

Docent in Structural Biology and Computational Biochemistry
Pharmaceutical Sciences Laboratory & Structural Bioinformatics Laboratory
Faculty of Science and Engineering
Åbo Akademi University
BioCity (3rd floor, Room 3027)
Tykistökatu 6A
20520 Turku, Finland
Tel + 358 2 2154006

Research areas

Structural Bioinformatics
1: Molecular Dynamics: Atomistic, Accelerated, Enhanced sampling, Metadynamics and Free-energy calculation
2: Molecular Modeling: Homology and ab-initio
3: Docking (protein-protein, protein-ligand) 
4: Virtual Screening (receptor / ligand based)
5: 3D-QSAR/Pharmacophore Modeling
6: Predictive modeling.

Current projects

My research topics focuses following targets
1. Bcl2 family proteins (Particularly, Mcl1 and Bcl-xL).
2. Simulation of CFTR channel with the pore blocker. (In col. Dr. Nagarajan OHSU).
3.​ Peptide binding mechanism investigation in Angiotensin II Receptor. (in col. Dr. Nagarajan OHSU).
4. In search of Ebola virus glycoprotein inhibitors using insilico approach. (in col. Prof. Outi Salo-Ahen).
5. Identifying novel antibacterial drugs against bacterial RNA Polymerase. (in col. Prof. Outi Salo-Ahen).
6. Anisomelic acid derivatives as HPV inhibitors. (in col. with Prof. Erikson's team).


  • March 2018 to to-date         Research Associate, Åbo Akademi University, Turku, Finland.

  • Feb 2017 to Dec 2017         Research Associate, Albany State University, Albany, Georgia, USA.

  • Dec-2010 to Jan 2017         Research Associate, Åbo Akademi University, Turku, Finland.

  • May 2010 to Oct 2010         Visiting scientist, Max-Plank Institute for molecular genetics (MolGen), Berlin,Germany.

  • June 2006 to Jan 2010        Ph.D. (Bioinformatics), Bharathiar University, Coimbatore, India.

  • Feb 2006 to June 2006        DBT (Department of Biotechnology -New Delhi) Research assistant (Bioinformatics)                                                   Pondicherry University, Pondicherry, India.

  • July 2004 to Jan 2006          Guest lecturer - Bioinformatics, Bharathiar University, India.

  • June 2002 to April 2004       M.Sc. (Bioinformatics), Bharathiar University, India.

  • June 1999 to April 2002       B.Sc. (Microbiology), Bharathidasan University, India.


1: Prof. Outi Salo-Ahen, Pharmacy, Åbo Akademi University, Turku, Finland.
2: Prof. Olli Pentikäinen, Institute of Biomedicine, University of Turku, Turku, Finland.

3: Prof. John Erikson, Biology, Åbo Akademi University, Turku, Finland.
3: Dr. Shanthi Nagarajan, OHSU, Portland, USA.
4: Dr. Jamoliddin Razzokov, Universiteit Antwerpen, Belgium.
5: Dr. Vigneshwaran Namasivayam, University of Bonn, Bonn, Germany
6: Dr. Pavithra Balasubramanian, Konkuk University, Seoul, Republic of Korea.
7: Dr. Manivel Palani, CSIR-CECRI, Tamil Nadu, India.

Oral presentations

  1. June 2020 "Computational methods as a tools towards pharmaceutical research" at Cresent Institute of Technology, Chennai, India. Webinar.

  2. June 2020 "Computational perspective towards pharmaceutical research" at Nehru college of arts and Science, Coimbatore, India. Webinar.

  3. Nov 2019 "Predicting hotspot residues and allosteric signal transmission mechanism in mouse pro-apoptotic peptide-Mcl1 complexes" at CompLifeSci, Turku.

  4. Nov 2019 "Disruption of conserved polar interactions causes sequential Bim mutants release from the cononical binding groove of Mcl1" at Uppsala University, Sweden.

  5. Oct 2019 "Unbinding simulation predicted the effect of point mutations in Bim peptide to downregulate Mcl1 activity " CSC, Espoo, Finland. (Flash)

  6. Mar 2017 “Molecular Dynamics Simulations applied to understand biomolecular behavior” at Albany State University, Georgia, USA.

  7. Nov 2016  “Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations” at Alagappa University, Tamil Nadu, India.

Poster presentations

1: Nov 2019 - Predicting hotspot residues and allosteric signal transmission mechanism in mouse pro-apoptotic peptide-Mcl1 complexes - CompLifeSci, Turku.

2: Nov 2019 - Disruption of conserved polar interactions causes sequential Bim mutants release from the cononical binding groove of Mcl1- Uppsala University, Uppsala, Sweden.

3: Aug 2019 - Unbinding simulation predicted the effect of point mutations in Bim peptide to downregulate Mcl1 activity - Biocity symposium, Turku, FI.
​4: Aug 2019 - Unbinding simulation predicted the effect of point mutations in Bim peptide to downregulate Mcl1 activity - BioExcel, Sardegna, Italy.
5: May 2017 - Molecular Properties Evaluation of Organophosphate Compounds to inhibit Acetylcholinesterase activity – An Insilico Approaches - University of Cincinatti, USA.
6: June 2016 - Probing the Hot spot residues for pro-apoptotic peptides—Mcl1 complex formation” - Åbo Akademi University, Finland.

Conferences & Workshops

1. CompLifeSci Annual meeting - UTU & ÅAU, Turku - 29.11.2019.

2. NordicPOP Workshop on Pharmaceutical Modelling and Simulation 2019 - Uppsala, Sweden.18-20 Nov 2019.

3. Schrödinger Maestro Hand-on workshop - CSC, Espoo, Finland. 7-8 Nov 2019.

4. Advanced Gromacs, HADDOCK + PMX workshop - CSC, Espoo, Finland. 9-10 Oct 2019.

5. BioExcel Summer School on Biomolecular Simulations 2019 – Sardegna, Italy. June 31 to July 5, 2019.
6. Pro-lipids 2019 Midsummer school, 10-13 June 2019- University of Helsinki and CSC, Finland.
7. Schrödinger Maestro Hands-on workshop - CSC, Espoo, Finland - 27 Nov 2018
8. Midsouth Computational Biology and Bioinformatics Society (MCBIOS2017) - FDA Arkansas, USA. 23-25 Mar 2017.
9. Pro-lipids 2015 spring school, 11-12 May 2015 - University of Helsinki, Finland.
10. CSC-spring school in Bioinformatics, 31 Mar - 3 Apr 2014 - CSC, Espoo, Finland.
11. X-ray course on Protein Crystallography Method, 16-20 Sept 2013 - University of Oulu, Finland.
12. Advanced Protein Expression and Characterization Course, 8-12 Oct 2012 - University of Helsinki, Finland.


1: Gabriel Pesavento, Erasmus + exchange student, Podovo, Italy (2013).
2: Morgan , Intern Student, Albany State University, Albany, USA (2017).
3: Tiffany Johnson, Intern Student, Albany State University, Albany, USA (2017).
4: Haley Evans, Intern Student, Albany State University, Albany, USA (2017).
5: Salim Baali, Visiting PhD student, University of Guelma, Algeria (2019).
6: Zeynep Pamukcu, Erasmus+ exchange student, Turkey (2019).
7: Nazia Hassan, MSc thesis worker, University of Turku, Turku, Finland (2019).
8: Anand Kalgudi, MSc thesis worker, University of Turku, Turku, Finland (2019).
9: Ville Järvinen, MSc thesis worker, Department of Physics, Åbo Akademi University, Turku, Finland (2019).

10. Paulina Frolovaite, MSc thesis worker, University of Turku, Turku, Finland (2020).


  1. Perumal M, Marimuthu P, Chen X. Investigation into the site-specific binding interactions between chlorogenic acid and ovalbumin using multi-spectroscopic and in silico simulation studies. J Biomol Struct Dyn. 2021 Feb 25:1-15. doi: 10.1080/07391102.2021.1886992.

  2. O.M.H. Salo-Ahen*, I. Alanko, R. Bhadane, A.M.J.J. Bonvin *, R. Vargas Honorato, S. Hossain, A.H. Juffer, A. Kabedev, M. Lahtela-Kakkonen, A. Støttrup Larsen, E. Lescrinier, P. Marimuthu, M. Usman Mirza, G. Mustafa, A. Nunes-Alve*, T. Pantsar, A. Saadabadi, K. Singaravelu, M. Vanmeert, Molecular dynamics simulations in drug discovery and pharmaceutical development. MDPI Processes 2021, 9(1), 71; https://doi.org/10.3390/pr9010071.

  3. Marimuthu P, Razzokov J, Singaravelu, K and Bogaerts, A. Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes. MDPI Biomolecules 2020, 10, 1114. https://doi.org/10.3390/biom10081114.

  4. Marimuthu P, Razzokov J and Eshonqulov G. ​Disruption of conserved polar interactions causes sequential Bim mutants release from the cononical binding groove of Mcl1. Int J Biol Macromol. 2020 May 158: 364-374. doi: 10.1016/j.ijbiomac.2020.04.243.

  5. Senthilkumar R, Brusentsev Y, P Paul, Marimuthu P, Cheng F, Eklund P, and Eriksson J. Synthesis and Evaluation of Anisomelic acid-like Compounds for the Treatment of HPV-Mediated Carcinomas. Sci Rep. 2019 Dec 30;9(1):20295. doi: 10.1038/s41598-019-56410-1.

  6. Singaravelu K*, Balasubramanian PK* and Marimuthu P. Investigating the Molecular Basis of N-Substituted 1-Hydroxy-4-Sulfamoyl-2-Naphthoate Compounds Binding to Mcl1. MDPI Processes. 2019 Apr 7(4), 224;  https://doi.org/10.3390/pr7040224

  7. Manivel P, Parthiban M, Ilanchelian M. Exploring the binding mechanism between methylene blue and ovalbumin using spectroscopic analyses and computational simulations. J Biomol Struct Dyn. 2019 Jun 4:1-10. doi: 10.1080/07391102.2019.1618734.

  8. Vignesh G, Parthiban M, Senthilkumar R, Arunachalam S. Molecular interaction studies of some Co(III)-surfactants with the transport protein. Colloids Surf B Biointerfaces. 2018 Sep 1;169:160-167. doi: 10.1016/j.colsurfb.2018.05.014.

  9. Marimuthu P, Singaravelu K. Unraveling the molecular mechanism of benzothiophene and benzofuran scaffold-merged compounds binding to anti-apoptotic Myeloid cell leukemia 1. J Biomol Struct Dyn. 2019 May;37(8):1992-2003. doi: 10.1080/07391102.2018.1474805.

  10. Marimuthu P, Singaravelu K. Prediction of Hot Spots at Myeloid Cell Leukemia-1-Inhibitor Interface Using Energy Estimation and Alanine Scanning Mutagenesis. Biochemistry. 2018 Feb 20;57(7):1249-1261. doi: 10.1021/acs.biochem.7b01048.

  11. Marimuthu P, Lee YJ, Kim B, Seo SS. In silico approaches to evaluate the molecular properties of organophosphate compounds to inhibit acetylcholinesterase activity in housefly. J Biomol Struct Dyn. 2019 Feb;37(2):307-320. doi: 10.1080/07391102.2018.1426046.

  12. Marimuthu P*, Balasubramanian PK*, Singaravelu K. Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein. J Biomol Struct Dyn. 2018 Aug;36(10):2654-2667. doi: 10.1080/07391102.2017.1365771.

  13. Marimuthu P, Singaravelu K. Deciphering the crucial residues involved in heterodimerization of Bak peptide and anti-apoptotic proteins for apoptosis. J Biomol Struct Dyn. 2018 May;36(6):1637-1648. doi: 10.1080/07391102.2017.1331863.

  14. Senthilkumar R*, Marimuthu P*, Paul P, Manojkumar Y, Arunachalam S, Eriksson JE, Johnson MS. Plasma Protein Binding of Anisomelic Acid: Spectroscopy and Molecular Dynamic Simulations. J Chem Inf Model. 2016 Dec 27;56(12):2401-2412. doi: 10.1021/acs.jcim.6b00445.

  15. Marimuthu P, Singaravelu K, Namasivayam V. Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations. J Biomol Struct Dyn. 2017 Dec;35(16):3507-3521. doi: 10.1080/07391102.2016.1260496.

  16. Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JA, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT, Hytönen VP. Zebavidin--an avidin-like protein from zebrafish. PLoS One. 2013 Oct 24;8(10):e77207. doi: 10.1371/journal.pone.0077207.

  17. Malinen AM, Turtola M, Parthiban M, Vainonen L, Johnson MS, Belogurov GA. Active site opening and closure control translocation of multisubunit RNA polymerase. Nucleic Acids Res. 2012 Aug;40(15):7442-51. doi: 10.1093/nar/gks383.

  18. Harbi D, Parthiban M, Gendoo DM, Ehsani S, Kumar M, Schmitt-Ulms G, Sowdhamini R, Harrison PM. PrionHome: a database of prions and other sequences relevant to prion phenomena. PLoS One. 2012;7(2):e31785. doi: 10.1371/journal.pone.0031785.

  19. Koshy C, Parthiban M, Sowdhamini R. 100 ns molecular dynamics simulations to study intramolecular conformational changes in Bax. J Biomol Struct Dyn. 2010 Aug;28(1):71-83.

  20. Parthiban M, Shanmughavel P, Sowdhamini R. In silico point mutation and evolutionary trace analysis applied to nicotinic acetylcholine receptors in deciphering ligand-binding surfaces. J Mol Model. 2010 Oct;16(10):1651-70. doi: 10.1007/s00894-010-0670-3.

  21. Parthiban M, Rajasekaran MB, Ramakumar S, Shanmughavel P. Molecular modeling of human pentameric alpha(7) neuronal nicotinic acetylcholine receptor and its interaction with its agonist and competitive antagonist. J Biomol Struct Dyn. 2009 Apr;26(5):535-47.

  22. Chandramoorthi GD, Piramanayagam S, Marimuthu P. An insilico approach to high altitude pulmonary edema - Molecular modeling of human beta2 adrenergic receptor and its interaction with Salmeterol & Nifedipine. J Mol Model. 2008 Sep;14(9):849-56. doi: 10.1007/s00894-008-0322-z.

  23. Parthiban M, Shanmughavel P. Three dimensional modeling of N-terminal region of galanin and its interaction with the galanin receptor. Bioinformation. 2007 Dec 5;2(3):119-25.

  24. Nagarajan S, Marimuthu P. Binding site prediction of galanin peptide using evolutionary trace method. Bioinformation. 2006 Jul 25;1(5):180-3.

  25. Marimuthu P, Rajasekaran MB, Shanmughavel P. Molecular docking and insilico analysis of angiogenesis inhibitor proteins. Bioinformatics India. 2005; 3: 1-5.

  26. Rajasekaran MB, Marimuthu P, Shanmughavel P. G-protein coupled receptors in drug discovery. SAJOSPS. 2005; 118-120.

* - Equal contribution

​Book Chapters

  1. Parthiban M, S. Susdalzew, S. Belsare, H. Stehr, M. Winkelmann, C. L. Sargent, E. Michalsky, M. Schneider, R. Preissner and M. Lappe (2010). "Homology Modeling of Protein Structure using Fragment/Profile based search method in CASP9" Critical assessment of methods for protein structure prediction (CASP9) - Abstract Book

  2. Parthiban M, Mohan Babu R, Shanmughavel P (2005), Bioinformatics tools to explore G Protein Coupled Receptors, Trends in Bioinformatics. (Ed) Dr. P.Shanmughavel, Pointer Publishers, Jaipur. India.