Dr. Sunil Kumar
Dr. Sunil Kumar
Principal Scientist
sunil.kumar7@icar.gov.in, skybiotech@gmail.com
Citations and H index

Area of Interest

  • Mainly focus on proteins with regard to their structures, functions, mutations and interactions.
  • Bioinformatics and Proteomics of Agricultural related problem.
  • Metagenomics and NGS.
  • Plant Microbe Interactions.

Ongoing Projects

  • Establishment of Centre for Bioinformatics and Computational Biology in Agriculture-BIC at ICAR-Indian Agricultural Statistics Research Institute at New Delhi (PI). Funded by DBT, Govt. of India.

  • Development of epsilon toxin based Novel vaccine against enterotoxaemia in goats: A bioinformatics assisted reverse vaccinology approach. Funded by ICAR

  • Genomics-assisted identification of trait- specific markers for major biotic and abiotic stresses and development of core collections of black pepper. Funded by ICAR

  • Improving Seed Health and Storage System. Funded by ICAR-- Inter-Institutional project

  • Mining agricultural microbiome datasets for Antibiotic Resistance Genes (ARG) diversity and prediction of microbial resistome –Inter-Institutional project

Completed Projects

  • Characterization of GSK3ß pathway in T-cell migration: Implications for novel immunomodulatory therapies, Funded by Ministry of Education, Singapore. (International collaborator)

  • Silver Ion Modulation of Glucose Mediated Respiration of E.Coli. Funded by Ministry of Higher education, Malaysia. (International collaborator)

  • Structure prediction, Molecular Dyanamics stimulations of endopolygalacturonase and its interaction with PGIP (polygalacturonase-inhibiting protein). Funded by ICAR

  • Design of Novel small molecule mimics binding to quorum sensors in Ralstonia Solanacearum. Funded by ICAR

  • Metatranscriptomics and metaproteomics analysis of wheat rhizosphere. Funded by ICAR

  • Deciphering Transcriptomic & Proteomic Changes in Stress-Challenged-Rice under Microbe-Interaction(s) to Explore Mitigation Strategies using Bioinformatics Approaches. Funded by ICAR

Foreign Visit

  • Malaysia
  • Singapore
  • Switzerland

Awards and Honours

  • Department of Biotechnology (DBT), Government of India nominated for participation in Indo-Malaysia Bilateral workshop and International Conference from 2-11 September, 2003 in Malaysia
  • Awarded travel support by Department of Biotechnology (DBT), Government of India to attend 8th International Conference on Bioinformatics (InCoB 2009) from 7-11 September 2009 in Singapore.
  • Awarded travel support by Department of Science & Technology (DST), Government of India to attend 8th Europeanl Conference on Computational Biology (ECCB) from 9-12 September 2012 in Basel, Switzerland.
  • Distinguished Scientist Award: by the society for Bioinformatics and Biological Sciences, Allahabad for the year 2015.
  • Fellow: Society of Applied Biotechnology (2016)
  • Fellow: Association of Biotechnology and Pharmacy(2016).
  • Best poster Award: 03
  • Best Paper Award: 01

Important Publications

  • Prabhakaran P, Hebbani AV, Menon SV, Paital B, Murmu S, Kumar S, Singh MK, Sahoo DK and Desai PPD (2023) Insilico generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CLpro) using deep learning. Front. Microbiol. 14:1194794. doi: 10.3389/fmicb.2023.1194794 (IF: 6.06) iconpdf

  • Choudhary P, Waseem M, Kumar S, Subbarao N, Srivastava S, Chakdar H (2023) Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study. World J Microbiol Biotechnol. 39(3):75. doi: 10.1007/s11274-023-03518-2. PMID: 36637534. (IF: 4.25). iconpdf

  • Kumar S*, Behera SK, Gururaj K, Chaurasia A, Murmu S, Prabha R, Angadi UB, Pawaiya RS, Rai A (2023) In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors. J Biomol Struct Dyn. 2:1-13. doi: 10.1080/07391102.2023.2204362. PMID: 37129165. iconpdf

  • Nagrale DT, Chaurasia A, Kumar S, Gawande SP, Hiremani NS, Shankar R, Gokte-Narkhedkar N, Renu, Prasad YG (2023) PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops. World J Microbiol Biotechnol. 16;39(4):100. doi: 10.1007/s11274-023-03536-0 iconpdf

  • Tyagi R, Paul A, Raj VS, Ojha KK, Kumar S*, Panda AK, Chaurasia A, Yadav MK (2023) A Drug Repurposing Approach to Identify Therapeutics by Screening Pathogen Box Exploiting SARS-CoV-2 Main Protease. Chem Biodivers. 20(2):e202200600.doi: 10.1002/cbdv.202200600 PMID: 36597267 iconpdf

  • Kumar S*, Ahmad K, Behera SK, Nagrale DT, Chaurasia A, Yadav MK, Murmu S, Jha Y, Rajawat MVS, Malviya D, Singh UB, Shankar R, Tripathy M, Singh HV (2022). Biocomputational Assessment of Natural Compounds as a Potent Inhibitor to Quorum Sensors in Ralstonia solanacearum. Molecules. 27(9):3034. doi: 10.3390/molecules27093034. PMID: 35566383; iconpdf

  • Malviya D, Singh UB, Dehury B, Singh P, Kumar M, Singh S, Chaurasia A, Yadav MK, Shankar R, Roy M, Rai JP, Mukherjee AK, Solanki IS, Kumar A, Kumar S* and Singh HV (2022) Novel Insights into Understanding the Molecular Dialogues between Bipolaroxin and the Gα and Gβ Subunits of the Wheat Heterotrimeric G-Protein during Host–Pathogen Interaction; Antioxidant; doi.org/10.3390/ antiox11091754 iconpdf

  • Vinita Ramtekey, Susmita C., Sunil Kumar, Sripathy K. V., Seema Sheoran, Udaya B. K., Bhojaraja N. K, Sanjay Kumar, Arvind N. Singh, Harsh Vardhan Singh (2022) Seed longevity in legumes: Deeper insights into mechanisms and molecular perspectives; Frontiers in Plant Science, doi.org/10.3389/fpls.2022.918206 (IF 6.6). iconpdf

  • Mahata S, Behera SK, Kumar S, Sahoo PK, Sarkar S, Fazil MHUT, Nasare VD. (2022) In-silico and in-vitro investigation of STAT3-PIM1 heterodimeric complex: Its mechanism and inhibition by curcumin for cancer therapeutics. Int J Biol Macromol. 208:356-366. doi: 10.1016/j.ijbiomac.2022.03.137.PMID: 35346675. (IF 8.05). iconpdf

  • Girdhar K, Thakur S, Gaur P, Choubey A, Dogra S, Dehury B, Kumar S, Biswas B, Dwivedi DK, Ghosh S, Mondal P. (2022) Design, synthesis, and biological evaluation of a small molecule oral agonist of the glucagon-like-peptide-1 receptor. J Biol Chem. 101889. doi: 10.1016/j.jbc.2022.101889. PMID: 35378127. iconpdf

  • Fazil MHUT, Chirumamilla CS, Perez-Novo C, Wong BHS, Kumar S, Sze SK, Vanden Berghe W, Verma NK. (2021) The steroidal lactone withaferin A impedes T-cell motility by inhibiting the kinase ZAP70 and subsequent kinome signaling. J Biol Chem. 2021:101377. doi: 10.1016/j.jbc.2021.101377. iconpdf

  • Yadav MK, Ahmad S, Raza K, Kumar S, Eswaran M, Pasha Km M (2021) Predictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2. J Biomol Struct Dyn. 1-13. doi: 10.1080/07391102.2021.2021993. PMID: 34974820. iconpdf

  • Jha Y, Dehury B, Kumar SPJ, Chaurasia A, Singh UB, Yadav MK, Angadi UB, Ranjan R, Tripathy M, Subramanian RB, Kumar S*, Simal-Gandara J (2021) Delineation of molecular interactions of plant growth promoting bacteria induced β-1,3-glucanases and guanosine triphosphate ligand for antifungal response in rice: a molecular dynamics approach. Mol Biol Rep doi: 10.1007/s11033-021-07059-5. iconpdf

  • Jaiswal S, Jagannadham J, Kumari J, Iquebal MA, Gurjar AKS, Nayan V, Angadi UB, Kumar S, Kumar R, Datta TK, Rai A and Kumar D (2021) Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo. Front. Vet. Sci. 8:593871. doi: 10.3389/fvets.2021.593871. iconpdf

  • Mishra P, Tandon G, Kumar M, Paital B, Swain SS, Kumar S, Samanta L (2021) Promoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line. J Biomol Struct Dyn. 31:1-20. doi: 10.1080/07391102.2021.1970624. iconpdf

  • Choubey A, Dehury B, Kumar S, Medhi B, Mondal P. (2020) Naltrexone a potential therapeutic candidate for COVID-19. J Biomol Struct Dyn. 15:1-8. doi: 10.1080/07391102.2020.1820379. . iconpdf

  • Choudhary P, Bhowmik A, Chakdar H, Khan MA, Selvaraj C, Singh SK Kumar M, Kumar S, Saxena AK (2020) Understanding the biological role of PqqB in Pseudomonas stutzeri using molecular dynamics simulation approach; J Biomol Struct Dyn; 8;1-13. doi: 10.1080/07391102.2020.1854860 iconpdf

  • Choudhary P, Chakdar H, Singh D, Selvaraj C, Singh SK, Kumar S, Saxena AK (2020) Computational studies reveal piperine, the predominant oleoresin of black pepper (Piper nigrum) as a potential inhibitor of SARS-CoV-2 (COVID-19);Current Science (00113891) . 10/25/2020, Vol. 119 Issue 8, p1333-1342. 10p

  • Kumar S, Dehury B, Tandon G, Jaiswal S, Iquebal MA, Ahmad K, Nagrale DT, Singh UB, Jha Y, Singh MK, Singh A, Rai A, Paital B, Kumar D (2020) Molecular interaction of PolyGalacturonase-Inhibiting Protein (PGIP), a leucine-rich repeat protein from banana with PolyGalacturonase (PG): A molecular dynamics prospect. Frontiers in Biosciences (Landmark Edition), 25:335-362; DOI: 10.2741/4809 iconpdf

  • Mishra P, Paital B, Jena S, Swain SS, Kumar S, Yadav MK, Chainy GBN, Samanta L (2019)Possible activation of NRF2 by Vitamin E/Curcumin against altered thyroid hormone inducedoxidative stress via NFĸB/AKT/mTOR/KEAP1 signalling in rat heart. Sci Rep. 9(1):7408. doi: 10.1038/s41598-019-43320-5. iconpdf

  • Ashutosh Kumar, Dinesh K. Agarwal, Sunil Kumar, Y. Mohan Reddy, Anjani Devi Chintagunta, K.V. Saritha, Govind Pal, S.P. Jeevan Kumar (2019) Nutraceuticals derived from seed storage proteins: Implications for health wellness, Biocatalysis and Agricultural Biotechnology;17: 710-719 doi.org/10.1016/j.bcab.2019.01.044. iconpdf

  • Choudhary P, Chakdar H, Singh A, Kumar S, Singh SK, Aarthy M, Goswami SK, Srivastava AK, Saxena AK (2019). Computational identification and antifungal bioassay reveals phytosterols as potential inhibitor of Alternaria arborescens. J Biomol Struct Dyn.; 38(4):1143-1157. doi: 10.1080/07391102.2019.1597767. iconpdf

  • Singh UB, Singh S, Malviya D, Singh S, Kumar M, Sahu PK, Singh HV, Kumar S, Roy M, Imran M, Rai JP, Sharma AK, and Saxena AK (2019) Trichoderma harzianum- and Methyl Jasmonate-Induced Resistance to Bipolaris sorokiniana Through Enhanced Phenylpropanoid Activities in Bread Wheat (Triticum aestivum L.) Front Microbiol. 2019; 10: 1697. doi: 10.3389/fmicb.2019.01697 iconpdf

  • Singh, U.B., Singh, S., Malviya, D. et al (2019) Integration of anti-penetrant tricyclazole, signaling molecule salicylic acid and root associated Pseudomonas fluorescens enhances suppression of Bipolaris sorokiniana in bread wheat (Triticum aestivum L.). J Plant Pathol 101, 943–954 (2019). https://doi.org/10.1007/s42161-019-00296-5 iconpdf

  • Sunil Kumar, MHU Turabe Fazil, Khursheed Ahmad, Minaketan Tripathy, and Navin Kumar Verma (2019) Computational Analysis of Protein-Protein Interactions in Motile T-cells; Methods in Molecular Biology; 2019;1930:149-156. doi: 10.1007/978-1-4939-9036-8_18. iconpdf

  • Chik MW, Hussain Z, Zulkefeli M, Tripathy M, Kumar S, Majeed ABA, Byrappa K (2019) Polymer-wrapped single walled carbon nanotubes: transformation toward better applications in healthcare. Drug Deliv Transl Res. 2018. doi: 10.1007/s13346-018-0505-9. iconpdf

  • Girdhar K, Dehury B, Singh MK, Daniel VP, Choubey A, Dogra S, Kumar S, Mondal P. (2018) Novel insights into the dynamics behavior of Glucagon-Like Peptide-1 Receptor with its small molecule Agonists; J Biomol Struct Dyn. 2018 Nov 17:1-11. doi: 10.1080/07391102.2018.1532818 iconpdf

  • Sunil Kumar*, Khurshid Ahmad, Gitanjali Tandon, Udai B. Singh, Yachana Jha, Dipak T. Nagrale, Mahender Kumar Singh, Khyati Girdhar, Prosenjit Mondal (2018) Novel insight into the molecular interaction of catalase and sucrose: A combination of in silico and in planta assays study. Computers and Electronics in Agriculture 151: 258-263.

  • Chakrapani V, Rasal KD, Kumar S, Mohapatra SD, Sundaray JK, Jayasankar P, Barman HK (2018). In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C. Interdiscip Sci.10(4):641-652. doi: 10.1007/s12539-017-0247-2. iconpdf

  • Verma NK, Fazil MH, Ong ST, Chalasani ML, Low JH, Kottaiswamy A, P P, Kizhakeyil A, Kumar S, Panda AK, Freeley M, Smith SM, Boehm BO, Kelleher D (2016) LFA-1/ICAM-1 ligation in T-cells promotes Th1 polarization through a GSK3β signalling-dependent Notch pathway; J Immunol. 2016 Jul 1;197(1):108-18. doi: 10.4049/jimmunol.1501264. iconpdf

  • Radin Nur Afiqah, Biswaranjan Paital, Sunil Kumar, Abu Bakar Abdul Majeed, Minaketan Tripathy (2016) AgNO3 Dependant Modulation of Glucose Mediated Respiration Kinetics in Escherichia coli at Different pH and Temperature. Journal of Molecular Recognition; 29(11):544-554, DOI: 10.1002/jmr.2554 iconpdf

  • Iquebal MA, Jaiswal S, Angadi UB, Sablok G, Arora V, Kumar S, Rai A and Kumar D (2015) SBMDb: First whole genome microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications" Database (Oxford). 8;2015. pii: bav111. doi: 10.1093/database/bav111. iconpdf

  • Paital B, Sablok G, Kumar S*, Singh SK, Chainy GB (2016). Investigating the Conformational Structure and Potential Site Interactions of SOD Inhibitors on Ec-SOD in Marine Mud Crab Scylla serrata: A Molecular Modeling Approach. Interdiscip Sci. 8(3):312-8. doi: 10.1007/s12539-015-0110-2. PMID: 26286009. iconpdf

  • Jha Y, Sablok G, Subbarao N, Sudhakar R, Fazil MH, Subramanian RB, Squartini A, Kumar S* (2014) Bacterial-induced expression of RAB18 protein in Orzya sativa salinity stress and insights into molecular interaction with GTP ligand. J Mol Recognit. 27(9):521-7. doi: 10.1002/jmr.2371. iconpdf

  • Tandon G, Jaiswal S, Iquebal MA, Kumar S, Kaur S, Rai A, Kumar D (2015) Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement. J Biomol Struct Dyn. 2015;33(10):2180-91. doi: 10.1080/07391102.2014.996187. iconpdf

  • Rawat R, Kumar S, Chadha BS, Kumar D, Oberoi HS. (2015) An acidothermophilic functionally active novel GH12 family endoglucanase from Aspergillus niger HO: purification, characterization and molecular interaction studies, Antonie van Leeuwenhoek, Journal of Microbiology; 107(1):103-17. doi: 10.1007/s10482-014-0308-z iconpdf

  • Norhafiza Razali, Renu Agarwal, Puneet Agarwal, Sunil Kumar, Minaketan Tripathy , Sushil Vasudevan, Jonathan G Crowston and Nafeeza M Ismail (2015) Role of adenosine receptors in resveratrol-induced IOP lowering in rats with steroid-induced ocular hypertension. Clinical and Experimental Opthalmology; 43(1):54-66 ; DOI: 10.1111/ceo.12375 iconpdf

  • Singh S, Sablok G, Farmer R, Singh AK, Gautam B, Kumar S.* (2013) Molecular dynamic simulation and inhibitor prediction of Cysteine synthase structured model as a potential drug target for Trichomoniasis. Biomed Res Int. 2013:390920. doi: 10.1155/2013/390920 iconpdf

  • Panda SK, Kumar S, Tupperwar NC, Vaidya T, George A, Rath S, Bal V, Ravindran B (2012) Chitohexaose Activates Macrophages by Alternate Pathway through TLR4 and Blocks Endotoxemia. PLoS Pathog 8(5): e1002717. doi:10.1371/journal.ppat. iconpdf

  • Kumar S*, Farmer R, Turnbull AP, Tripathy NK, Manjasetty BA (2012) Structural and functional conservation profiles of novel cathepsin L-like proteins identified in the Drosophila melanogaster genome. J Biomol Struct Dyn. 2013 Dec;31(12):1481-9. doi: 10.1080/07391102.2012.745379. Epub 2012 Dec 21. PMID: 23256878. iconpdf

  • Fazil MH, Kumar S, Rao NS, Selvaraj C, Singh SK, Pandey HP, Singh DV (2012) Comparative structural analysis of two proteins belonging to quorum sensing system in Vibrio cholerae. J Biomol Struct Dyn.;30(5):574-84. doi: 10.1080/07391102.2012.687523. iconpdf

  • Indu Joshi, Sunil Kumar, Arminder Kaur, C.S. Mukhopadhyay and Dinesh Kumar (2012) Homology Modeling Of Buffalo (Bubalus Bubalis) Interferon-Tau Protein. American Journal of Bioinformatics, 1 (2): 79-86, 2012

  • Biswaranjan Paital, Sunil Kumar*, Rohit Farmer, Gagan Bihari Nityananda Chainy (2013) In silico prediction of 3D structure of Mn superoxide dismutase of Scylla serrata and its binding properties with inhibitors, Interdiscip Sci Comput Life Sci 2013 Mar; 5(1):69-76. doi: 10.1007/s12539-013-0150-4. iconpdf

  • Alok Das Mohapatra, Sunil Kumar, Ashok Kumar Satapathy and Balachandran Ravindran (2011).Caspase Dependent Programmed Cell Death in Developing Embryos: A Potential Target for Therapeutic Intervention against Pathogenic Nematodes. PloS Neglected Tropical Disease 5(9): e1306. doi:10.1371/journal.pntd.0001306. iconpdf

  • Fazil MH, Kumar S, Farmer R, Pandey HP, Singh DV. (2011). Binding efficiencies of carbohydrate ligands with different genotypes of cholera toxin B: Molecular Modeling, dynamics and Docking Simulation studies. J Mol Model, 18(1):1-10. doi: 10.1007/s00894-010-0947-6. iconpdf

  • Biswaranjan Paital, Sunil Kumar*, Rohit Farmer, Niraj Kanti Tripathy, Gagan Bihari Nityananda Chainy (2011) In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdiscip Sci Comput Life Sci 3: 110–120

  • Mohapatra C, Barman HK, Panda RP, Kumar S, Das V, Mohanta R, Mohapatra SD, Jayasankar P. Cloning of cDNA and prediction of peptide structure of Plzf expressed in the spermatogonial cells of Labeo rohita. Mar Genomics. 2010 Sep-Dec;3(3-4):157-63. doi: 10.1016/j.margen.2010.09.002. iconpdf

  • MHU Turabe Fazil*, Sunil Kumar*, N Subbarao, H P Pandey and Durg V. Singh (2010). Homology modeling of a sensor histidine kinase from Aeromonas hydrophila. J Mol Model, 16: 1003-1009

Book Edited:

  • S Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (Eds.) Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches (Springer) ISBN 978-3-319-17156-2

Book /Manual Chapters

  • Jaiswal, S., Iquebal, M.A. , Angadi U.B. , Kumar, S., Rai, A., Singh, N.K., Kumar, D.(2021) Mango Genomic Resources and Databases. In: Kole C. (eds) The Mango Genome. Compendium of Plant Genomes. Springer, Cham. Book Chapter The Mango Genome pp 219-228,iconpdf

  • Dipak T. Nagrale, Lalan Sharma and Sunil Kumar (2016) Recent diagnostics and detection tools: Implications for plant pathogenic Alternaria and their disease management (2016). P. Kumar et al. (eds.), Current Trends in Plant Disease Diagnostics and Management Practices, Fungal Biology, DOI 10.1007/978-3-319-27312-9_5; ISBN : 978-3-319-27310-5 (Springer International Publishing Switzerland). iconpdf

  • Sunil Kumar (2018) Protein ligand Interaction by Performing Docking Studies. Tomar R. S., Parakhia M.V, Bhat S.B and Golakiya B.A. (Eds) 2018 Genomic, Proteomic and Metabolomic Application in Crop Improvement. Department og Biotechnology, Junagadh Agricultural University, Junagadh-362001, Gujarat. India. ISBN:978-93-86546-79-1; Page No.221

  • Sunil Kumar (2018) Comparative Modeling. Tomar R. S., Parakhia M.V, Bhat S.B and Golakiya B.A. (Eds) 2018 Genomic, Proteomic and Metabolomic Application in Crop Improvement. Department og Biotechnology, Junagadh Agricultural University, Junagadh-362001, Gujarat. India. ISBN:978-93-86546-79-1; Page No.237

  • MHU Turabe Fazil, K. Konda Reddy, H P Pandey and Sunil Kumar (2017) Molecular Modeling and Drug Design: A Contemporary Analysis in Vibrio cholera. Current trends in Bioinformatics: An Insight ( Wadhwa, G., Shanmughavel, P., Singh, A.K., Bellare, J.R. (Eds.)) Springer Nature, ISBN:978-981-10-7481-3

  • MHU Turabe Fazil, Sunil Kumar and Durg V singh. In Silico Analysis of Sequence Variation in Cholera Toxin B Subunit and Their Binding with Carbohydrate Ligands. In Current Topics in Biotechnology & Microbiology. Dhingra Hk, Jha PN and Bajpai P (Eds), Lap Lambert Academic publishing AG & Co. KG, Dudweller, Landstr Germany, 2011, Pg 168-177. ISBN 978-3-8443-2975-9.

  • Partha Sarathi Das, Sunil Kumar and Bikas R. Pati (2015) nifH Database: Insights into Diversity and Evolution to Explore Next Generation Nitrogen Fixer. "Recent Trends in Biofertilizers" ISBN 978-93-84588-65-6; IK International Delhi.

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