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Dr. Parthiban Marimuthu, Ph.D.

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
Email: parthiban.marimuthu@abo.fi
 
 

Research areas

Structural Bioinformatics
1: Molecular Dynamics
2: Molecular Modeling
3: Docking and Virtual Screening of ligands
4: 3D-QSAR/Pharmacophore Modeling, Predictive modeling.

Current projects

1. Bcl2 family proteins
2. Simulation of CFTR channel with the pore blocker.
3.​ Peptide binding mechanism investigation in Angiotensin II Receptor 1.

Education

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.

Colloborations

1: Prof. Outi Salo-Ahen, Pharmacy, Åbo Akademi University, Turku, Finland.
2: Prof. Olli Pentikäinen, Institute of Biomedicine, University of Turku, 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: Mar 2017 “Molecular Dynamics Simulations applied to understand biomolecular behavior” at Albany State University, Georgia, USA.
2: 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: Parthiban Marimuthu  (Aug 2019) “Unbinding simulation predicted the effect of point mutations in Bim peptide to downregulate Mcl1 activity” at Biocity symposium, Turku, FI.
​2: Parthiban Marimuthu  (Aug 2019) “Unbinding simulation predicted the effect of point mutations in Bim peptide to downregulate Mcl1 activity” at BioExcel, Sardegna, Italy.
3: Parthiban Marimuthu and Yong Jin Lee (May 2017) “Molecular Properties Evaluation of Organophosphate Compounds to inhibit Acetylcholinesterase activity – An Insilico Approaches” at University of Cincinatti, USA.
4: Parthiban Marimuthu and Kalaimathy Singaravelu (June 2016) “Probing the Hot spot residues for pro-apoptotic peptides—Mcl1 complex formation” at Åbo Akademi University, Finland.

Conferences & Workshops

1. BioExcel Summer School on Biomolecular Simulations 2019 – June 31 to July 5, 2019.
2. Pro-lipids 2019 Midsummer school, June10-13, 2019, at University of Helsinki and CSC, Finland.
3. Schrödinger Maestro Hands-on workshop, at CSC Finland - 27.11.2018
4. Midsouth Computational Biology and Bioinformatics Society – MCBIOS2017 March 23-25, 2017.
5. Pro-lipids 2015 spring school, May11-12, 2015, at University of Helsinki, Finland.
6. CSC-spring school in Bioinformatics, 31-March-2014 to 3-April 2014, at CSC, Helsinki, Finland.
7. X-ray course on Protein Crystallography Method, 16-20th   September 2013, at University of Oulu, Finland.
8. Advanced Protein Expression and Characterization Course, 8-12th Oct 2012, at University of Helsinki, Finland.

Supervision

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 graduate student, University of Guelma, Algeria (2019).
6: Zyenep Pamukcu, Erasmus + exchange student, Turkey, (2019).
7: Nasia Hassan, Masters intern, University of Turku, Turku, Finland (2019).
8: Anand Kalgudi, Masters intern, University of Turku, Turku, Finland (2019).
9: Ville Järveinen, Department of Physics, Master intern, University of Turku, Turku, Finland (2019).

Publications

1: 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; doi: https://doi.org/10.3390/pr7040224

2: 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.

3: 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.

4: 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.

5: 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.

6: 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.

7: 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.

8: 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.

9: 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.

10: 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.

11: 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.

12: 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.

13: 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.

14: 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.

15: 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.

16: 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.

17: 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.

18: 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.

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

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

21: 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.

 

© 2016 Pharmaceutical Sciences Laboratory

Offical University Website:

https://www.abo.fi/amnen/farmaci/

Pharmaceutical Sciences

Åbo Akademi University

BioCity 3rd floor

Artillerigatan 6A

FI 20520 Turku

Finland

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