Dr. Konda Mani SARAVANAN Ph.D.

Assistant Professor
Department of Biotechnology
Bharath Institute of Higher Education & Research 
Chennai - 600 073, Tamilnadu, India

mobile: +91 9790254267

 

Brief Bio

I am happy to introduce myself as an independent researcher in Bioinformatics and Computational Biology. I got the University First Rank in M.Sc. Bioinformatics and went onto complete my Ph.D. Bioinformatics from Bharathidasan University under the supervision of Dr. S. Selvaraj. I then joined Prof. S. Krishnaswamy’s research group at Madurai Kamaraj University in 2013 under the distinguished UGC Dr DS Kothari Post-doctoral fellowship. Subsequently I have joined for Post-doctoral work with Prof. P. Karthe at University of Madras. I was awarded the competitive DST-SERB National Post-doctoral fellowship (2016-2018). From 2018-2020, I joined a well funded Post-doctoral fellowship position at Prof. Yanjie Wei’s group at Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, China. After that I went on to gain industrial experience (SCIGEN Research & Innovation and B-Aatral Biosciences), where I provide Bioinformatics support to experimental researchers doing different projects. I have long and rich post-doctoral research experience and my productivity is seen by the more than 80 peer reviewed research publications. I also have successful collaborations with diverse research groups as evidenced by publications with scholars from different countries.

Education & Work Experience

B.Sc         - (1999-2002) Mathematics (AVVM Sri Pushpam College, Thanjavur)
M.Sc         - (2002-2004) Bioinformatics (Annai College of Arts & Science, Kumbakonam)
Trainee      - (2004-2005) Bioinformatics Tool Development (Zeneca Biotech Pvt Ltd, Chennai)
Lecturer     - (2005-2007) Bioinformatics (Annai College of Arts & Science, Kumbakonam)
M.Phil       - (2007-2008) Biotechnology (Alagappa University, Karaikudi)
Ph.D         - (2008-2013) Bioinformatics (Bharathidasan University, Tiruchirappalli)
PostDoc1     - (2013-2016) Transmembrane Proteins (Madurai Kamaraj University, Madurai)
PostDoc2     - (2016-2018) Intrinsic Disordered Proteins (University of Madras, Chennai)
PostDoc3     - (2018-2020) Membrane Protein Structure Prediction (Chinese Academy of Sciences, PR China)
Scientist    - (2020-2021) GPCR proteins (Scigen Research & Innovation Pvt Ltd, Thanjavur)
Scientist    - (2021-2021) E3 ligases (B-Aatral Biosciences, Bengaluru)
Asst Prof    - (2021-Till) Bharath Institute of Higher Education & Research, Chennai

Awards & Fellowships

University First Rank in M.Sc. Bioinformatics (April 2004)
DST-Junior Research Fellowship (3.10.2007-17.11.2009)
DST-JST Senior Research Fellowship (18.11.2009-31.3.2010)
CSIR-Direct Senior Research Fellowship (1.4.2010-6.3.2013)
UGC's Dr DS Kothari Post Doctoral fellowship (4.6.2013-3.6.2016)
DST-SERB National Post Doctoral Fellowship (6.6.2016-5.6.2018)
SIAT-CAS Post Doctoral Fellowship (1.7.2018-28.10.2020)
SIAT-CAS CBB Lab Best Presentation Award (6.1.2020)

Memberships

Life Member, Indian Biophysical Society (IBS)
Life Member, China Artificial Intelligence Society of Bioinformatics (CAAI)
Member, China Computer Federation (CCF)
Regional Student Member, International Society of Computational Biology (ISCB)
Life Member, Institute of Scholars (InSc)
Non-academia Member, Board of Studies in Bioinformatics, University of Madras, Chennai.
Deputy Editor in Chief, International Journal of Biotechnology & Clinical Medicine.
Frontiers Topic Editor, AI in the drug discovery pipeline of tropical diseases.
Guest Editor, Artificial intelligence and Computer-Aided Drug Discovery: Methods development and application.
Series Editor, Futuristic Trends in Biotechnology, IIP Series.
Editorial Board Member, Medinformatics, Bon View Publishing Limited.

Editorial Activities

Current Science, Journal of Medicinal Chemistry, Future Medicinal Chemistry, Methods, Molecular Biotechnology, Cells, Cancers, Big data mining and analytics, Biochemical and Biophysical Research Communications, Frontiers in Molecular Biosciences, Frontiers in Medicine, PLoS One, Genes, Gene, Molecules, Biomolecules, Biology, Viruses, Computers in Biology & Medicine, Computational Structural Biotechnology Journal, Cell Biochemistry & Biophysics, Journal of Medical Virology, The Protein Journal, Heliyon, Computational and Theoretical Chemistry, Oncotargets and Therapy, Journal of Biomolecular Structure & Dynamics, Acta Tropica, Interdisciplinary Sciences, International Journal of Molecular Sciences, Life, Biomedinformatics, Pathogens; Biotechnology and Applied Biochemistry, Journal of Clinical Medicine, Reactions, Metabolites, Drug Design Development & Therapy, COVID, Frontiers in Public Health, Advances in Public Health, Applied Sciences, Pharmaceuticals, International Nano Letters, Future Science OA, Journal of Pure and Applied Microbiology, Journal of Education and Health Promotion, Letters in Applied Bionanoscience, Biointerface Research in Applied Chemistry, AIMS Biophysics, Ecological Genetics and Genomics, IOP Proceedings, Journal of Environmental Pathology, Toxicology & Oncology, Gene Reports, Indian Journal of Science and Technology, Journal of Natural Products & Biomedical Research, Journal of Pharmacological & Toxicological Investigations, The Scientific pages of kinetics & Thermodynamics, Biomedical and Biotechnology Research Journal, Journal of Reports in Pharmaceutical Sciences, Asia Pacific Journal of Science and Technology, International Journal of Nutrition Pharmacology Neurological Diseases, Biotechnologia, Journal of Applied Biology & Biotechnology, Qeios, Medinformatics, OBM Genetics, Journal of Microbiology Biotechnology and Food Sciences, IIP Proceedings, Scientific Journal of Health Science Research, Computer methods in Biomechanics and Biomedical Engineering.


Bioinformatics Tools

DeepGPCR - GPCR-ligand predictions for high precision drug discovery.

DeepToxicity - A deep learning based multimodel approach to predict drug like chemical's toxicity.

DeepBindGCN - Integrating molecular vectors with Graph CNN model for predicting protein-ligand interaction and affinity.

Therapeutic Peptide Generator - A deep learning based therapeutic peptides generation and screening.

Denovo chemicals Generator - Generating and screening de novo chemical compounds using ultrafast deep learning models.

DeepBindBC - A deep learning method to identify native-like protein-ligand complexes.

DeepBindPoc - A deep learning method to accurately identify and rank ligand binding pockets.

DeepBindRG - A deep learning method for estimating effective protein-ligand affinity.

PreFRP - Prediction and visualization of fluctuation amino acid residues in proteins.


Selected publications (Cumulative JCR Impact factor - 308.34)

B. Harihar, K.M. Saravanan, M.M. Gromiha and S. Selvaraj (2024). Importance of inter residue interactions for understanding protein folding and unfolding rates, remote homology and drug design. Molecular Biotechnology  In Press.

R. Senthil, G. Archunan, D. Vithya and K.M. Saravanan (2024). Hexadecanoic acid analogs as potential CviR-mediated quorum sensing inhibitors in Chromobacterium violaceum: an in silico study. Journal of Biomolecular Structure & Dynamics In Press.

S.R. Pandi-Perumal, K.M. Saravanan, S. Paul, G.P. Namasivayam and S.B. Chidambaram (2024).  Waking up the sleep field: An overview on the implications of genetics and bioinformatics of sleep. Molecular Biotechnology  In Press.

H. Zhang and K.M. Saravanan (2024). Advances in deep learning assisted drug discovery methods: A self review. Current Bioinformatics  In Press.

A. Murugesan, K.M. Saravanan, S. Koochakkhani, K. Subramanian, J. Kandhavelu, R. Thiyagarajan, A. Gurbanov, K.T. Mahmudov and M. Kandhavelu  (2024). Design, synthesis and anticancer evaluation of novel arylhydrazones of active methylene compounds. International Journal of Biological Macromolecules  254, 127909.

J. Kandhavelu, K. Subramanian, V. Naidoo, G. Sebastianelli, P. Doan, K.M. Saravanan, H. Yapislar, E. Haciosmanoglu, L. Arslan, S. Ozer, R. Thiyagarajan, N.R. Candeias, C. Penny, M. Kandhavelu and A. Murugesan (2024). A novel EGFR inhibitor, HNPMI regulates apoptosis and oncogenesis by modulating BCL-2/BAX and P53 in colon cancer. British Journal of Pharmacology  16141, 1-18.

G. Bupesh, C. Amutha, K.M. Saravanan, S. Sudharsan, K.M. Sundaram, T. Siva Vijayakumar, P.P. Pankaj, G. Archunan, D. Haripriya and U.K. Sahoo (2024). Characterization of novel antimicrobial peptides from the epidermis of Clarias batrachus catfish. International Journal of Peptide Research & Therapeutics 30, 11.

S.R. Pandi Perumal, W.A.C.M. van de Put, A. Maercker, S.E. Hobfoll, V. Mohan Kumar, C. Barbui, A.M. Mahalakshmi, S.B. Chidambaram, O. Lundmark, T.S. Khai, L. Atwoli, V. Poberezhets, R. Rajesh Kumar, D. Madoro, H.A.M. Agudelo, S.R.H. Hoole, L. Teixeira-Santos, P. Pereira, K.M. Saravanan, A. Vrdoljak, M.M. Cruz, C. Ramasubramaniam, A.K. Tay, J. Gronli, M. Sijbrandij, S. Sivasubramaniam, N. Meera, E.N. Mbong, M. Jansson-Frojmark, B. Bjorvatn, J.T. de Jong, M.H. Braakman, M. Eisenbruch, A.C. Dario, K. van der Velden, G.M. Brown, M. Partinen, A.C. McFarlane and M. Berk  (2023). Harbingers of hope: Scientists and the pursuit of world peace. Clinical Psychology in Europe 5, e13197. 

A. Murugesan, K.M. Saravanan, T. Ramesh, S. Palanivel, A.V. Gurbanov, F.I. Zubkov and M. Kandhavelu  (2023). Benzenesulfonamide analogs: Synthesis, anti-GBM activity and pharmacoprofiling. International Journal of Molecular Sciences  24, 12276.

H. Zhang, K.M. Saravanan and John ZH Zhang (2023). DeepBindGCN: Integrating molecular vector representation with graph convolutional neural networks for accurate protein-ligand interaction prediction. Molecules 28, 4691.

K. Mayuri, S. Sarojini, S.S. Chaitanya, R.B.S. Kushwah, K.M. Saravanan, V. Sundaram and T. Anand (2023). Advancement of targeted protein degradation strategies as therapeutics for undruggable disease targets. Future Medicinal Chemistry 15, 867-883.

K.M. Saravanan*, T. Ramesh, O. Yli-Harja, M. Kandhavelu and A. Murugesan (2023). Structural analysis of human G-Protein-Coupled Receptor17 ligand binding sites. Journal of Cellular Biochemistry 124, 533-544.

S. Sarojini, K. Mayuri, R.B.S. Kushwah, V. Sundaram, V. Alaguraj, T. Anand and  K.M. Saravanan* (2023). Drug design and disease diagnosis: The potential of deep learning models in biology. Current Bioinformatics 18, 208-220.

A. Murugesan, K. Sana, A. Shreshtha, B. Assoah, K.M. Saravanan, M. Murugesan, T. Ramesh, N. Candeias and M. Kandhavelu  (2023). Methanodibenzo[b,f][1,5]dioxocins as novel glutaminase inhibitor with antiglioblastoma potential. Cancers  15, 1010.

H. Zhang, K.M. Saravanan, Y. Wei, Y. Jiao, Y. Yang, Y. Pan, X. Wu and John ZH Zhang (2023). Deep learning based bioactive therapeutic peptides generation and screening. Journal of Chemical Information & Modeling 63, 835-845.

P. Kamaraj, V.V. Sridhar, T.S. Vijayakumar, S. Parthasarathy, G. Bupesh, N.K. Raju, U.K. Sahoo, A. Nandha and K.M. Saravanan (2023). Carbon nanoparticles fabricated microfilm: A potent filter for microplastics debased water. Environment Pollution 336, 122502.

G. Mutharasu, A. Murugesan, K.M. Saravanan, T. Ramesh, O. Yli-Harja and M. Kandhavelu (2023). Signaling landscape of mitochondrial non-coding RNAs. Journal of Biomolecular Structure & Dynamics 41, 12016-12025.

H. Zhang, K.M. Saravanan, Y. Yang, Y. Wei, Y. Pan and John ZH Zhang (2022). Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. Briefings in Bioinformatics  23, bbac226.

K.M. Sundaram, A. Vamsi Kumar, T. Alphonsa, R. Sangeetha, R. Krishnamurthy, A. Alemtoshi, V. Balachander, B. Pranjal, G. Bupesh and K.M. Saravanan*(2022). COVID-19 and Tuberculosis: Two knives in a sheath. Coronaviruses  3, e050722206645.

H. Zhang, T. Zhang, K.M. Saravanan, L. Liao, H. Wu, H. Zhang, H. Zhang, Y. Pan, X. Wu, Y. Wei  (2022). DeepBindBC: A practical deep learning method for identifying native-like protein-ligand complexes. Methods  205, 247-262.

G. Pothiaraj, M. Manoranjini, S. Pitchaikani, K.K. Gowtham, K.M. Saravanan, M. Rajan and H. Shakila (2022). Investigation of therapeutic and immunomodulatory activity of Bacopa Saponin (Bacopa Monnieri). South African Journal of Botany 151, 639-650.

H. Zhang, G.X. Hua, Y. Peng, K.M. Saravanan, Z. Bian, Z. Zhang, Y. Wei, Y. Pan and Y. Yang (2022). An efficient modern  strategy to screen drug candidates targeting RdRp of SARS-CoV-2 with potentially high selectivity and specificity. Frontiers in Chemistry  10, 933102.

Y. Feng, X. Cheng, S. Wu, K.M. Saravanan and W. Liu (2022). Hybrid drug screening strategy identifies potential SARS-CoV-2 cell entry inhibitors targeting human transmembrane serine protease. Structural Chemistry  33, 1503-1515.

K.M. Saravanan, M. Kannan, P. Meera, N. Bharathkumar and T. Anand (2022). E3 ligases: a potential multi drug target for different types of cancers and neurological disorders. Future Medicinal Chemistry 14, 187-201.

N. Bharathkumar, A. Sunil, P. Meera, S. Aksah, M. Kannan, K.M. Saravanan and T. Anand (2022). CRISPR/Cas based modifications for therapeutic applications: a review. Molecular Biotechnology 64, 355-372.

K.M. Saravanan, H. Zhang, R. Senthil, K.K. Vijayakumar, V. Sounderarajan, Y. Wei and H. Shakila (2022). Structural basis for the inhibition of SARS-CoV2 main protease by Indian medicinal plant derived antiviral compounds. Journal of Biomolecular Structure & Dynamics 40, 1970-1978.

R. Senthil, K.M. Sundaram, G. Bupesh, S. Usha and K.M. Saravanan* (2022). Identification of oxazolo[4,5-g]quinazolin-2(1H)-one derivatives as EGFR inhibitors for cancer prevention. Asian Pacific Journal of Cancer Prevention 23, 1687-1697.

A. Murugesan, P. Nguyen, T. Ramesh, O. Yli-Harja, M. Kandhavelu and K.M. Saravanan* (2022). Molecular modelling and dynamics studies of the synthetic small molecule agonists with GPR17 and P2Y receptor. Journal of Biomolecular Structure & Dynamics 40, 12908-12916.

H. Zhang, J. Li, K.M. Saravanan, H. Wu, Z. Wang, D. Wu, Y. Wei, Z. Lu, Y.H. Chen, X. Wan and Y. Pan (2021). An integrated deep learning and molecular dynamics simulations based screening pipeline identifies inhibitors of a new cancer drug target TIPE2. Frontiers in Pharmacology 12, 772296.

H.T. Le, A. Murugesan, T. Ramesh, O. Yli-Harja, K.M. Saravanan* and M. Kandhavelu(2021). Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis. International Journal of Biological Macromolecules 189, 142-150.

P. Nguyen, P. Doan, T. Rimpilainen, K.M. Saravanan, A. Murugesan, O. Yli-Harja, N.R. Candeias and M. Kandhavelu (2021). Synthesis and pre-clinical validation of novel indole derivatives as a GPR17 agonist for glioblatoma treatment. Journal of Medicinal Chemistry 64, 10908-10918.

H. Zhang, Z. Bei, W. Xi, M. Hao, Z. Ju, K.M. Saravanan, H. Zhang, N. Guo and Y. Wei (2021). Evaluation of residue-residue contact prediction methods: from retrospective to prospective. PLoS Computational Biology 17, e1009027.

P. Doan, P. Nguyen, A. Murugesan, K. Subramanian, K.M. Saravanan, V. Kalimuthu, B.G. Abraham, B. Stringer, K. Balamuthu, O. Yli-Harja and M. Kandhavelu (2021). Targeting orphan G-Protein Coupled Receptor 17 with T0 ligand impairs glioblastoma growth. Cancers 13, 3773.

K.M. Saravanan, H.P. Zhang, H.L. Zhang, W. Xi and Y. Wei (2020). On the conformational dynamics of β-amyloid forming peptides: a computational perspective. Frontiers in Bioengineering & Biotechnology 8, 532.

H. Zhang, Y. Yang, J. Li, M. Wang, K.M. Saravanan, J. Wei, Ng. Justin, Md. T. Hossain,  M. Liu, H. Zhang, X. Ren, Y. Pan, Y. Peng, Y. Shi, X. Wan, Y. Liu and Y. Wei (2020). A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro. PLoS Computational Biology 16, e1008489.

H. Zhang, K.M. Saravanan, Y. Yang, Md. T. Hossain, J. Li, X. Ren, Y.Pan and Y. Wei (2020). Deep learning based drug screening for novel Coronavirus 2019-nCov. Interdisciplinary Sciences 12, 368-376.

H. Zhang, K.M. Saravanan, J. Lin, L. Liao, N.T.Y. Justin, J. Zhou and Y. Wei (2020). DeepBindPoc: A deep learning method to rank ligand binding pockets using molecular vector representation. Peer J 8, e8864.

K.M. Saravanan, Y. Peng and Y. Wei (2020). Systematic analysis of no regular secondary structural regions(NORS) in membrane and non-membrane proteins. Journal of Biomolecular Structure & Dynamics 38, 268-274.

A. Viswanathan, A. Musa, A. Murugesan, J.R. Vale, C.A.M. Afonso, K.M. Saravanan, O. Yli-Harja, N.R. Candeias and M. Kandhavelu (2019). Battling Glioblastoma: A novel tyrosine kinase inhibitor with multi-dimensional anti-tumor effect. Cells 8, 1624.

H. Zhang, X. Shao, Y. Peng, Y. Teng, K.M. Saravanan, H. Zhang, H. Li and Y. Wei (2019). A novel machine learning based approach for iPS progenitor cell identification. PLoS Computational Biology 15, e1007351.

H. Zhang, L. Liao, K.M. Saravanan, Y. Peng and Y. Wei (2019). DeepBindRG: a deep learning based method for estimating effective protein-ligand affinity. Peer J 7, e7362.

K.M. Saravanan and K. Ponnuraj (2019). Sequence and structural analysis of fibronectin binding proteins reveals the importance of multiple intrinsic disordered tandem repeats. Journal of Molecular Recognition 32, e2768.

H. Le, T. Rimpilainen, K.M. Saravanan, A. Murugesan, O. Yli-Harja, N.R. Candeias and M. Kandhavelu (2019). Synthesis and pre-clinical validation of novel P2Y receptor ligands as a potent anti-prostate cancer agent. Scientific Reports 9, 18938.

A. Viswanathan, D. Kute, A. Musa, K.M. Saravanan, V. Sipila, F. Emmert-Streib, F. Zubkov, A.V. Gurbanov, O. Yli-Harja and M. Kandhavelu (2019). 2-(2-(2,4-dioxopentan-3-ylidene)hydrazineyl)benzonitrile as novel inhibitor of receptor tyrosine kinase and PI3K/AKT/mTOR signaling pathway in glioblastoma. European Journal of Medicinal Chemistry 166, 291-303.

K.M. Saravanan, A.K. Dunker and S. Krishnaswamy (2018). Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions. Journal of Biomolecular Structure & Dynamics 36, 4338-4351.

K.M. Saravanan, S. Palanivel, O. Yli-Harja and M. Kandhavelu (2018). Identification of novel GPR17-agonists by Structural Bioinformatics and signaling activation. International Journal of Biological Macromolecules 106, 901-907.

A. Viswanathan, A. Zhurina, B. Assoah, A. Paakkunainen, A. Musa, D. Kute, K.M. Saravanan, N.R. Candeias and M. Kandhavelu (2018). Decane-1,2-diol derivatives as potential antitumor agents for the treatment of glioblastoma. European Journal of Pharmacology 837, 105-116.

K.M. Saravanan and S. Selvaraj (2017). Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins. Journal of Biological Physics 43, 265-278. 

K. Ponnuraj and  K.M. Saravanan* (2017). Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins. International Journal of Biological Macromolecules 97, 434-439.

P. Manoharan and K.M. Saravanan* (2017). Computational profiling of pore properties of outer membrane proteins. Journal of Biomolecular Structure & Dynamics  35, 2372-2381.

K.M. Saravanan, S. Suvaithenamudhan, S. Parthasarathy and S. Selvaraj (2017). Pairwise contact energy statistical potentials can help to find probability of point mutations. Proteins: Structure Function & Bioinformatics 85, 54-64.

K.M. Saravanan and S. Krishnaswamy (2015). Dihedral angle preferences for alanine and glycine residues in alpha and beta transmembrane regions. Journal of Biomolecular Structure & Dynamics 33, 552-562. 

K.M. Saravanan and S. Selvaraj (2013). Performance of secondary structure prediction methods on proteins containing structurally ambivalent sequence fragments. Biopolymers 100, 148-153. 

K.M. Saravanan and S. Selvaraj (2013). Search and analysis of identical reverse octapeptides in unrelated proteins. Genomics Proteomics Bioinformatics 11, 114-121. 

K.M. Saravanan and S. Selvaraj (2012). Search for identical octapeptides in unrelated proteins: Structural plasticity revisited. Biopolymers 98, 11-26. 

K.M. Saravanan, H. Balasubramanian, S. Nallusamy and S. Selvaraj (2010). Sequence and Structural analysis of two designed proteins with 88% identity adopting different folds. Protein Engineering Design & Selection 23, 911-918.