Dr. Narendra Kumar
Research Interest:
Summary of Research:Computational Immunology, Immunoinformatics, Computational Genomics, Elucidation of gene regulatory networks.
Computational Immunology and Immunoinformatics
Recent COVID-19 pandemic has highlighted the urgency to quickly respond to new infectious agents, and develop therapeutics and preventive strategies in a reasonable time to minimize the loss of life. Vaccines are most effective preventive measures in containing the infectious diseases. Our lab is interested in better understanding the principles and molecular mechanisms governing the antigen specificity to be used in rational design of vaccines. We will use the molecular structure (experimental and models) and sequence data (NGS) in public databases to understand complex interplay of T-cell receptor binding to antigen-MHC complex and effects of genetic variation. We will develop computational tools, algorithms, pipelines, and databases of immunological importance to be used by research community.
Understanding chromatin site targeting by transcription factors
Transcriptionally inactive chromatin is packed in nucleosomes that resists the binding of transcription factors. However, certain transcription factors can still access their target sites to open the chromatin and initiate transcription. Our interest is in understanding how such transcription factors access their binding motifs in the chromatin using structure modelling based approaches in conjunction is NGS based high throughput data. Availability of nucleosome positioning data, x-ray structures of transcription factors and ChIP-seq of transcription factors in public databases give opportunities to understand gene regulation. We will develop computational tools for analysis of gene regulation.
Publications:
- Manisha Shukla, Pankaj Chandley, Suman Tapryal, Narendra Kumar, Sulakshana P. Mukherjee and Soma Rohatgi (2022) Expression, purification and refolding of Chikungunya virus full length envelop E2 protein along with B-cell and T-cell epitope analysis using immuno-informatics approaches. ACS Omega 7: 3491-3513
- Ashok Kumar, Gaobing Wu, Zuo Wu, Narendra Kumar and Ziduo Liu (2018) Improved catalytic properties of a serine hydroxymethyl transferase from Idiomarina loihiensis by site directed mutagenesis. International journal of biological macromolecules 117: 1216-1223.
- Shradha Khater, Money Gupta, Priyesh Agrawal, Neetu Sain, Jyoti Prava, Priya Gupta, Mansi Grover, Narendra Kumar and Debasisa Mohanty (2017) SBSPKSv2: Structure based sequence analysis of polyketide syntheses and non-ribosomal peptide synthetases. Nucleic Acids Research 45:W72-W79
- Narendra Kumar, Nikhil Damle and Debasisa Mohanty (2015) Getting phosphorylated: Is it necessary to be accessible? Proc Indian Natn Sci Acad Part A 81:493-507.
- Narendra Kumar and Jeffrey Skolnick (2012) EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics 28:2687-2688.
- Anwar Ahmed, Kavita Gaadhe, Guru Prasad Sharma, Narendra Kumar, Mirela Neculai, Raymond Hui, Debasisa Mohanty, Pushkar Sharma (2012) Novel insights into the regulation of malarial calcium-dependent protein kinase 1. The FASEB Journal 26:3212-3221.
- Swadha Anand, Prasad Manglam, Gitanjali Yadav, Narendra Kumar, Jyoti Shehara, Zeeshan Ansari and Debasisa Mohanty (2010) SBSPKS: Structure Based Sequence Analysis of Polyketide Synthases. Nucleic Acids Research 38:W487-96.
- Narendra Kumar and Debasisa Mohanty (2010) Structure-based identification of MHC binding peptides: Benchmarking of prediction accuracy. Molecular Biosystems 12:2508-20.
- Narendra Kumar and Debasisa Mohanty (2010) Identification of substrates for Ser/Thr protein kinases using residue based statistical pair potentials. Bioinformatics 26:189-197.
- Narendra Kumar and Debasisa Mohanty (2007) MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. Nucleic Acids Research 35:W549-555.
