Dr. Aditya Kumar Padhi

Assistant Professor
Department/School/Unit Name
School of Bio-chemical Engg., IIT(BHU)
Phone No(s): .
Email: aditya.bce@iitbhu.ac.in
Area of Interest: Computational Biology, Structural & Translational Bioinformatics, Computational Biophysics, Protein Design, Predictive Modeling, Biomolecular Modeling and Simulations, Conformational Analyses, Machine Learning, Disease Mechanisms

Education

Ph.D., Indian Institute of Technology Delhi (IIT Delhi), India
Computational Biology

B.Tech., Biju Patnaik University of Technology (BPUT), Odisha, India
Biotechnology
 

Academic Experience

Assistant Professor (June 2022 - Present)
School of Biochemical Engineering
Indian Institute of Technology (BHU), Varanasi, India

Postdoctoral Researcher
(JSPS & TBRF fellow)
Laboratory for Structural Bioinformatics
Center for Biosystems Dynamics Research
RIKEN, Yokohama, Japan

Citations: 1200+; h-index: 18; i10-index: 26 (*Corresponding author)

Research & Review Papers (Peer-reviewed)

48. Amar Jeet Yadav, Shivank Kumar, Shweata Maurya, Khushboo Bhagat, Aditya K. Padhi* (2024) Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design, Physical Chemistry Chemical Physics. 26(18):14046-14061 (IF: 3.676)[Selected for the PCCP 2023 Emerging Investigators-Themed Issue].

47. Deeksha Dewangan, Aryaman Joshi, Aditya K. Padhi* (2024) Long-Timescale Atomistic Simulations Uncover Loss-of-Function Mechanisms of Uncharacterized Angiogenin Mutants Associated with ALS, Archives of Biochemistry and Biophysics. doi:10.1016/j.abb.2024.110000 (IF: 3.9).

46. Shweata Maurya, Shivank Kumar, Aditya K. Padhi* (2023) Interface-Guided Computational Protein Design Reveals Bebtelovimab-Resistance Mutations in SARS-CoV-2 RBD: Correlation with Global Viral Genomes and Bebtelovimab-Escape Mutations, ChemistrySelectdoi: 10.1002/slct.202302906 (IF: 2.1).

45. Aditya K. Padhi*, Parismita Kalita, Shweata Maurya, Krishna Mohan Poluri, Timir Tripathi (2023) From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics, ACS Journal of Physical Chemistry B. 127(41):8717-8735. doi:10.1021/acs.jpcb.3c04542 (IF: 3.3).

44. Aryaman Joshi, Shweata Maurya, Atharva Mahale, Soumya Lipsa Rath, Timir Tripathi, Aditya K. Padhi* (2023) Delineating the Structure–Dynamics–Binding Differences among BA.1, BA.4/5, and BF.7 SARS-CoV-2 Variants through Atomistic Simulations: Correlation with Structural and Epidemiological Features, ACS Omega, https://doi.org/10.1021/acsomega.3c02904 (IF: 4.1).

43. Jingjie Chang, Motoi Yamashita, Aditya K. Padhi, Kam Zhang, Ichiro Taniuchi (2023) Impaired tissue homing by the Ikzf3 N159S variant is mediated by interfering with Ikaros function, Frontiers in Immunology [official journal of the International Union of Immunological Societies (IUIS)], 14:1239779, doi:10.3389/fimmu.2023.1239779 (IF: 7.3).

42. Sushma Subedi, Niharika Nag, Harish Shukla, Aditya K. Padhi, Timir Tripathi (2023) Comprehensive analysis of liquid–liquid phase separation propensities of HSV-1 proteins and their interaction with host factors, Journal of Cellular Biochemistry, https://doi.org/10.1002/jcb.30480 (IF: 4.0).

41. Parismita Kalita, Timir Tripathi, Aditya K. Padhi* (2023) Computational Protein Design for COVID-19 Research and Emerging Therapeutics, ACS Central Science, https://doi.org/10.1021/acscentsci.2c01513 (IF: 18.728).

40. Aryaman Joshi, Timir Tripathi, Sumit K. Singh, Aditya K. Padhi* (2023) Computational Approaches for Development of Engineered Therapeutics against SARS-CoV-2, ACS Biochemistry, https://doi.org/10.1021/acs.biochem.2c00629 (IF: 3.321).

39. Indrajeet Yadav, Akhil Rautela, Agendra Gangwar, Vigya Kesari, Aditya K. Padhi, Sanjay Kumar (2023) Geranyl Diphosphate Synthase (CrtE) Inhibition Using Alendronate Enhances Isoprene Production in Recombinant Synechococcus elongatus UTEX 2973: A Step towards Isoprene Biorefinery, Fermentation, 9(3):217, https://doi.org/10.3390/fermentation9030217 (IF: 5.123).

38. Rupal Ojha, Satyendra Singh, Nidhi Gupta, Ketan Kumar, Aditya K. Padhi, Vijay Kumar Prajapati (2023) Multi-pathogen based chimeric vaccine to fight against COVID-19 and concomitant coinfections, Biotechnology Letters, May 6. doi: 10.1007/s10529-023-03380-0 (IF: 2.716).

37. Debaprasad Koner, Niharika Nag, Parismita Kalita, Aditya K. Padhi, Timir Tripathi, Nirmalendu Saha (2023) Functional expression, localization, and biochemical characterization of thioredoxin glutathione reductase from air-breathing magur catfish, Clarias magur, International Journal of Biological Macromolecules, 230:123126. doi:10.1016/j.ijbiomac.2022.123126 (IF: 8.025).

36. Aditya K. Padhi*, Timir Tripathi (2022) Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes, Biochemical and Biophysical Research Communications, https://doi.org/10.1016/j.bbrc.2022.09.010 (IF: 3.322).

35. Aditya K. Padhi*, Timir Tripathi (2022) A comprehensive protein design protocol to identify resistance mutations and signatures of adaptation in pathogens, Briefings in Functional Genomics, DOI: https://doi.org/10.1093/bfgp/elac020 (IF: 4.840).

34. Aditya K. Padhi*, Timir Tripathi (2022) High-throughput Designing of Symmetrical Dimeric SARS-CoV-2 Main Protease: Structural and Physical Insights into Hotspots for Adaptation and Therapeutics, Physical Chemistry Chemical Physics, DOI: https://doi.org/10.1039/D2CP00171C (IF: 3.945).

33. Nabanita Mandal, Aditya K. Padhi, Soumya Lipsa Rath (2022) Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern, Journal of Molecular Graphics and Modelling, 2022 Apr 14;114:108194. DOI: 10.1016/j.jmgm.2022.108194 (IF: 2.942).

32. Soumya Lipsa Rath, Aditya K. Padhi, Nabanita Mandal (2022) Scanning the RBD-ACE2 molecular interactions in Omicron variant, Biochemical and Biophysical Research Communications, 592, 18-23. DOI: https://doi.org/10.1016/j.bbrc.2022.01.006 (IF: 3.322).

31. Sota Yagi, Aditya K. Padhi, Jelena Vucinic, Sophie Barbe, Thomas Schiex, Rieko Nakagawa, David Simoncini*, Kam Y. J. Zhang*, Shunsuke Tagami* (2021) Seven amino acid types suffice to create the core fold of RNA polymerase, Journal of the American Chemical Society, 143, 39, 15998–16006. DOI: 10.1021/jacs.1c05367 (IF: 16.383).

  • Press Release: 
  • https://www.riken.jp/en/news_pubs/research_news/rr/20220127_1/index.html
  • https://bdrtimes.riken.jp/en/2022/04/04/syagi/

30. Aditya K. Padhi, Ashutosh Kumar, Ken-ichi Haruna, Haruna Sato, Hiroko Tamura, Satoru Nagatoishi, Kouhei Tsumoto, Atushi Yamaguchi, Fumie Iraha, Mihoko Takahashi, Kensaku Sakamoto*, Kam Y. J. Zhang* (2021) An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes, Briefings in Bioinformatics, bbab338, https://doi.org/10.1093/bib/bbab338 (IF: 13.994).

29. Aditya K. Padhi, Jagneshwar Dandapat, Prakash Saudagar, Vladimir N. Uversky, and Timir Tripathi (2021) Design of favipiravir-binding site in SARS-CoV-2 RdRp unravels susceptible hotspots and resistance mutations: a focus on chain-termination mechanism, FEBS Letters, 595(18):2366-2382. DOI: https://doi.org/10.1002/1873-3468.14182 (IF: 3.864).

28. Purna B Chetri, Rohit Shukla, Javed M Khan, Aditya K. Padhi, and Timir Tripathi (2021) Unraveling the Structural Basis of Urea-induced Unfolding of Fasciola gigantica Cytosolic Malate Dehydrogenase, Journal of Molecular Liquids, https://doi.org/10.1016/j.molliq.2021.118170 (IF: 6.633).

27. Motoi Yamashita, Hye Sun Kuehn, Kazuki Okuyama, Satoshi Okada, Yuzaburo Inoue, Noriko Mitsuiki, Kohsuke Imai, Masatoshi Takagi, Hirokazu Kanegane, Masahiro Takeuchi, Naoki Shimojo, Miyuki Tsumura, Aditya K. Padhi, Kam Y. J. Zhang, Bertrand Boisson, Jean-Laurent Casanova, Osamu Ohara, Sergio D. Rosenzweig, Ichiro Taniuchi, Tomohiro Morio (2021) A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS, Nature Immunology, https://doi.org/10.1038/s41590-021-00951-z (IF: 31.25).

  • Press Release:
  • RIKEN: https://www.riken.jp/press/2021/20210622_2/index.html
  • Tokyo Medical and Dental University: https://www.tmd.ac.jp/pressrelease/202100621_1/
  • https://scienmag.com/when-mad-aiolos-drags-ikaros-down-a-novel-pathogenic-mechanism/
  • https://www.sciencedaily.com/releases/2021/07/210716112503.htm

26. Aditya K. Padhi, Soumya Lipsa Rath, and Timir Tripathi (2021) Accelerating COVID-19 Research Using Molecular Dynamics Simulation, ACS Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.1c04556 (IF: 3.466). [Selected for the cover page of JPCB, issue 33 (dated 8/26/21)].

25. Aditya K. Padhi*, Rohit Shukla, Priyam Narain, James Gomes (2021) A distant Angiogenin variant causes amyotrophic lateral sclerosis through loss-of-function mechanisms: Insights from long-timescale atomistic simulations and conformational dynamics, Computers in Biology and Medicine, https://doi.org/10.1016/j.compbiomed.2021.104602 (IF: 6.698).

24. Aditya K. Padhi*, Timir Tripathi (2021) Targeted Design of Drug Binding Sites in the Main Protease of SARS-CoV-2 Reveals Potential Signatures of Adaptation, Biochemical and Biophysical Research Communications, https://doi.org/10.1016/j.bbrc.2021.03.118 (IF: 3.322).

23. Aditya K. Padhi, Rohit Shukla, Prakash Saudagar, Timir Tripathi (2021) High-throughput Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance, iScience, 101992 (IF: 6.107).

22. Sourya Bhattacharya, Abhilek K Nautiyal, Rajanya Bhattacharjee, Aditya K. Padhi, Vivek Junghare, Muskaan Bhambri, Diptarka Dasgupta, Thallada Bhaskar, Debashish Ghosh, Saugata Hazra (2021) A comprehensive characterization of novel CYP-BM3 homolog (CYP-BA) from Bacillus aryabhattai, Enzyme and Microbial Technology, https://doi.org/10.1016/j.enzmictec.2021.109806 (IF: 3.705).

21. Aditya K. Padhi, Kam Y.J. Zhang (2020) Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis, Scientific Reports, 10, 17146. DOI: https://doi.org/10.1038/s41598-020-74048-2 (IF: 4.996).

20. Sourya Bhattacharya, Aditya K. Padhi, Vivek Junghare, Neeladrisingha Das, Debashish Ghosh, Partha Roy, Kam Y.J. Zhang, Saugata Hazra (2021) Understanding the molecular interactions of beta-lactamase inhibitors against Bla1 beta-lactamase towards unraveling the mechanism of antimicrobial resistance, International Journal of Biological Macromolecules, https://doi.org/10.1016/j.ijbiomac.2021.02.069 (IF: 8.025).

19. Aditya K. Padhi, Aniruddha Seal, Javed Masood Khan, Maqusood Ahamed, Timir Tripathi (2020) Unraveling the mechanism of arbidol binding and inhibition of SARS-CoV-2: Insights from atomistic simulations, European Journal of Pharmacology, 173836 (IF: 5.195).

18. Aditya K. Padhi, Timir Tripathi (2020) Can SARS-CoV-2 Accumulate Mutations in the S-Protein to Increase Pathogenicity? ACS Pharmacology & Translational Science, https://doi.org/10.1021/acsptsci.0c00113 (IF: NA).

17. Parismita Kalita, Aditya K. Padhi, Kam Y.J. Zhang, Timir Tripathi (2020) Design of a Peptide-Based Subunit Vaccine against Novel Coronavirus SARS-CoV-2, Microbial Pathogenesis, https://doi.org/10.1016/j.micpath.2020.104236 (IF: 3.848).

16. Aditya K. Padhi, Parismita Kalita, Kam Y.J. Zhang, Timir Tripathi (2020) High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19, BioRxiv, https://doi.org/10.1101/2020.05.19.104042 (IF: NA).

15. Jupitara Kalita, Aditya K. Padhi, Timir Tripathi (2020) Designing a vaccine for fascioliasis using immunogenic 24 kDa mu-class glutathione s-transferase, Infection, Genetics and Evolution, https://doi.org/10.1016/j.meegid.2020.104352 (IF: 4.393).

14. Aditya K. Padhi*, Priyam Narain, James Gomes (2019) Rare Angiogenin and Ribonuclease 4 variants associated with amyotrophic lateral sclerosis exhibit loss-of-function: A comprehensive in silico study, Metabolic Brain Disease, DOI: 10.1007/s11011-019-00473-6 (IF: 3.655).

13. Priyam Narain, Aditya K. Padhi, Upma Dave, Dibyakanti Mishra, Rohit Bhatia, Perumal Vivekanandan, James Gomes (2019) Identification and characterization of novel and rare susceptible variants in Indian Amyotrophic Lateral Sclerosis patients, Neurogenetics, 20(4):197–208 (IF: 3.017).

12. Parismita Kalita, Denzelle Lee Lyngdoh, Aditya K. Padhi, Harish Shukla, Timir Tripathi (2019) Development of multi-epitope driven subunit vaccine against Fasciola gigantica using immunoinformatics approach, International Journal of Biological Macromolecules, https://doi.org/10.1016/j.ijbiomac.2019.07.024 (IF: 8.025).

11. Aditya K. Padhi*, James Gomes (2019) A molecular dynamics-based investigation reveals the role of rare Ribonuclease 4 variants in amyotrophic lateral sclerosis susceptibility, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 813, 1-12 (IF: 3.151).

10. Kornélia Tripolszki, Judit Danis, Aditya K. Padhi, James Gomes, Renáta Bozó, Zsófia F. Nagy, Dóra Nagy, Péter Klivényi, József I. Engelhardt, Márta Széll (2019) Angiogenin mutations in Hungarian patients with amyotrophic lateral sclerosis: clinical, genetic, computational and functional analyses. Brain and Behavior, e01293. doi: 10.1002/brb3.1293 (IF: 3.405).

9. Aditya K. Padhi*, Saugata Hazra (2018) Insights into the role of D-amino acid oxidase mutations in amyotrophic lateral sclerosis. Journal of Cellular Biochemistry. DOI:10.1002/jcb.27529 (IF: 4.48).

8. Aditya K. Padhi, Priyam Narain, Upma Dave, Rohit Satija, Anirudh Patir, James Gomes (2017) Insights into the role of Ribonuclease 4 polymorphisms in Amyotrophic Lateral Sclerosis. Journal of Biomolecular Structure and Dynamics, 1102, 1-15 (IF: 5.235).

7. Aditya K. Padhi, Kamalika Banerjee, James Gomes, Manidipa Banerjee (2014) Computational and Functional Characterization of Angiogenin Mutations, and Correlation with Amyotrophic Lateral Sclerosis. PLoS ONE, 9(11), e111963 (IF: 3.752).

6. Ashutosh Shukla, Aditya K. Padhi, James Gomes, Manidipa Banerjee (2014) The VP4 peptide of Hepatitis A Virus (HAV) Ruptures Membranes through Formation of Discrete Pores. Journal of Virology, 01896-14 (IF: 6.549).

5. Aditya K. Padhi, Suhas V. Vasaikar, B. Jayaram, James Gomes (2014) ANGDelMut – a web-based tool for predicting and analyzing functional loss mechanisms of amyotrophic lateral sclerosis-associated angiogenin mutations. F1000Research, 2:227 (IF: NA).

4. Aditya K. Padhi, Suhas V. Vasaikar, B. Jayaram, James Gomes (2013) Fast prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis. FEBS Letters, 587(12), 1762-1766 (IF: 3.864).

3. Suhas V. Vasaikar, Aditya K. Padhi, B. Jayaram, James Gomes (2013) NeuroDNet - an open-source platform for constructing and analyzing neurodegenerative disease networks. BMC Neuroscience, 14(1), 3 (IF: 3.264).

2. Aditya K. Padhi, B. Jayaram, James Gomes (2013) Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations. Scientific Reports, 3, 1225 (IF: 4.996).

1. Aditya K. Padhi, Hirdesh Kumar, Suhas V. Vasaikar, B. Jayaram, James Gomes (2012) Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis. PLoS ONE, 7(2), e32479 (IF: 3.752). [Among the top 25% of most-cited PLoS ONE articles].

Conference Proceedings

2. Aditya K. Padhi, B. Jayaram, James Gomes (2013) A molecular dynamics simulation-based prediction of deleterious angiogenin mutations causing amyotrophic lateral sclerosis. Journal of Biomolecular Structure and Dynamics, 31(sup1), 103.

1. Suhas V. Vasaikar, Aditya K. Padhi, B. Jayaram, James Gomes (2011) Network Analysis of Neurodegenerative Diseases: A System-based Approach to Uncover Perturbed Networks. Frontiers in Neuroinformatics, 5.

Book Chapters

3. Aditya K. Padhi*, Shweata Maurya (2024) Uncovering the Secrets of Resistance: An Introduction to Computational Methods in Infectious Disease Research, Advances in Protein Chemistry and Structural Biology. doi: https://doi.org/10.1016/bs.apcsb.2023.11.004 (In press) (IF: 5.447).

2. Parismita Kalita, Aditya K. Padhi, Timir Tripathi (2022) Immunoinformatics Protocol to Design Multi-epitope Subunit Vaccines. Methods in Molecular Biology, Springer, 2673:357-369. doi:10.1007/978-1-0716-3239-0_25 (IF: NA).

1. Aditya K. Padhi, Matej Janežič, Kam Y. J. Zhang (2022) Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics. The book, “Advances in Protein Molecular and Structural Biology Methods,” Academic Press, Elsevier, USA, 439-454 [ISBN: 978-032-39-0264-9] (IF: NA).

Awards & Honors

  1. Alexander Fleming Young Scientists Award by the Biofootprints Society, India for the Year 2023.
  2. Bioinformatics and Drug Discovery Society (BIDDS) India Young Scientist Award for the Year 2022.
  3. Selected as a Postdoctoral Fellow (top 50 candidates worldwide) for IndiaBioscience’s PDF Meeting 2021.
  4. Selected as a Postdoctoral Fellow for IndiaBioscience’s 13th Young Investigator Meeting 2021.
  5. Tokyo Biochemical Research Foundation (TBRF) International Fellowship Program – 2019 for conducting research in Japan.
  6. Takeda Science Foundation International Fellowship Program – 2019 for conducting research in Japan (Awarded but Not Availed).
  7. Japan Society for Promotion of Science (JSPS) Postdoctoral Research Fellowship – 2017 for conducting research in Japan.
  8. Recipient of Grants-in-Aid for Scientific Research (KAKENHI) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, for the fiscal year 2018 to 2021.
  9. Distinction in Doctoral Research Award at IIT Delhi for excellence in Ph.D. research – 2016 (Given to the top 10% of the graduate students in a calendar year).
  10. Travel grant from Indian Council of Medical Research (ICMR), Govt. of India, for poster presentation at the “Gordon Research Conference on Protein Folding Dynamics – From the Computer to the Cell: Protein Folding, Function and Evolution” at Galveston, Texas, USA (2014).
  11. Travel grant from Department of Biotechnology (DBT), Govt. of India, for oral & poster presentations at the “Albany 2013: Conversation 18” at the State University of New York at Albany (2013) (Awarded but Not Availed).
  12. Travel grant from the Department of Science and Technology (DST), Government of India, for oral & poster presentations at the “Albany 2013: Conversation 18” at the State University of New York at Albany (2013).
  13. Senior Research Fellowship (SRF) from the Council of Scientific & Industrial Research (CSIR), New Delhi, India (2013 – 2016) for doctoral studies.
  14. Selected among the top 20 teams for idea presentation at Association of Biotechnology Led Enterprises (ABLE) - BEST-India (Biotechnology Entrepreneurship Student Teams), Bangalore, sponsored by the Department of Biotechnology (DBT), India (2012).

Membership

  1. Life member of Biophysical Society, Rockville, Maryland, USA.
  2. Life member of the Indian Biophysical Society (IBS), India.
  3. Life member of Bioinformatics and Drug Discovery Society (BIDDS), India.
  4. Life member of Biofootprints Society, India.
  5. American Association for Advancement of Science (AAAS).
  6. Life member of the Society of Neurochemistry (SNCI), India.
  7. Life member of the Association of Biotechnology Led Enterprises (ABLE), India.

Editor & Reviewer for Journals

As Editor

  • Editor: Biochemical and Biophysical Research Communications (Elsevier)
  • Editorial Advisory Board: FEBS Letters (Wiley)
  • Academic Editor: PLOS ONE
  • Youth Editorial Board Member: hLife (Elsevier)
  • Review Editor: Frontiers in Molecular Biosciences, Structural Biology Section

As Reviewer

  • Royal Society of Chemistry: (1) Physical Chemistry Chemical Physics
  • American Chemical Society: (1) Journal of Medicinal Chemistry, (2) The Journal of Physical Chemistry, (3) ACS Omega
  • Wiley: (1) Advanced Science; (2) Protein Science; (3) Journal of Cellular Biochemistry; (4) ChemistrySelect
  • Oxford University Press: (1) Briefings in Bioinformatics, (2) Briefings in Functional Genomics
  • Elsevier: (1) International Journal of Biological Macromolecules; (2) Computational and Structural Biotechnology Journal; (3) Drug Discovery Today; (4) Computers in Biology and Medicine; (5) Chemical Physics; (6) Journal of Molecular Liquids; (7) Immunobiology; (8) Infection, Genetics and Evolution; (9) Journal of Molecular Structure; (10) Journal of Fluorine Chemistry; (11) Arabian Journal of Chemistry; (12) Informatics in Medicine Unlocked; (13) Computer Methods and Programs in Biomedicine Update; (14) Saudi Journal of Biological Sciences; (15) Molecular Immunology; (16) Gene; (17) Molecular Pathogenesis; (18) Biosensors and Bioelectronics
  • Nature Publishing Group: (1) Scientific Reports
  • Springer: (1) Cellular and Molecular Biochemistry; (2) Metabolic Brain Disease; (3) Journal of Cancer Research and Clinical Oncology; (4) Drugs in R&D
  • Taylor & Francis: (1) Journal of Biomolecular Structure and Dynamics; (2) Annals of Medicine
  • Cell Press: (1) Heliyon
  • Frontiers: (1) Frontiers in Molecular Biosciences; (2) Frontiers in Molecular Neuroscience; (3) Frontiers in Cell and Developmental Biology; (4) Frontiers in Pharmacology
  • Future Medicine: (1) Future Microbiology; (2) Future Virology
  • PeerJ
  • International Scientific Information: (1) Medical Science Monitor
  • Bentham Science: (1) Current Protein and Peptide Sciences

Laboratory for Computational Biology & Biomolecular Design (LCBD)

The broad research themes of the Laboratory for Computational Biology & Biomolecular Design (LCBD) at BCE, IIT(BHU) are in the areas of “Computational Protein & Enzyme Design”, “Protein Engineering”, “Large-Scale Mutational Analysis”, “Health Informatics & Therapeutics Development”, “Tools, Pipelines Development”. Our overarching research goal focuses on two major directions: (1) Fundamental and translational research & (2) Methods, pipelines, and tools development.
 
In “Fundamental and translational research”, we develop & utilize (i) Computational Protein Design (CPD) approaches to understand the evolution and emergence of certain macromolecular machines of metabolic, therapeutic, and biotechnological significance. Further, we investigate the (ii) structure-dynamics-function of complex biological systems, employing integrated approaches & gain fundamental knowledge about the determinants of molecular function. Specifically, the goal is to perform large-scale analyses of disease-causing genetic variations, SNPs, rare variants, and conformational analyses through multi-combinatorial approaches.
           
In “Methods, pipelines and tools development”, we (i) design high-affinity protein binders of therapeutic and biotechnological significance, (ii) implement non-natural amino acids in proteins and other biomolecules for affinity prediction & maturation, (iii) develop CPD methods with improved scoring functions and for accounting protein flexibility, and (iv) analyzing & predicting disease-causing/susceptible mutations. For some of these studies, we collaborate with fellow experimental biologists and chemists.
           
Lately, we have also been working on COVID-19, where we predict and comprehend the complexity of several SARS-CoV-2 proteins, drug target interactions, and resistance-causing mutations employing exhaustive CPD strategies, molecular dynamics simulations complemented with mutational mapping, and other computational biophysics techniques to provide insight into the functional outcome of mutations in the SARS-CoV-2 proteins and disease pathophysiology.

Si. No.

Student

Degree

Year

Research Area

Status

1 Amar Jeet Yadav PhD August 2023 Computational protein design of prototype folds Ongoing
2 Khushboo Bhagat PhD August 2023 Design-structure-function relationship of key effectors Ongoing
3 Sonia Sarangi PhD (JDP Scholar with IIT Guwahati) August 2023 Electrochemical Aptamer-Based Sensors Designing Ongoing

4

Shweata Maurya

M.Tech

December 2022

Computational protein design approaches in deciphering resistance mutations

Ongoing

5 Akshit M.Tech December 2023 Computational protein design approaches to comprehend SARS-CoV-2-mediated pathophysiology Ongoing
6 Dhruv Rawat IDD Exploratory August 2023 Molecular simulations in understanding aggregation of disease-causing proteins Ongoing
7 Karishma Santani IDD Exploratory August 2023 Understanding the molecular mechanisms of kinase loss-of-functions in neurodegenerative disorders Ongoing

8

Shivank Kumar

IDD UG

January 2023

Development of integrated machine-learning pipelines

Ongoing

9

Anany Sharma

IDD UG

January 2023

Employing machine learning methods to identify resistance mutations in mAbs against their bound targets

Ongoing

10

Deeksha Dewangan

IDD Exploratory

August 2022

Insights into the role of rare variants in neurodegeneration

Ongoing

11

Aryaman Joshi

B.Tech

June 2022

Understanding the mechanisms of engineered therapeutics for diverse applications

Completed

Year 2023-24 (Even Semester)

  1. Molecular Biology & Genetic Engineering (BC - 332)
  2. Molecular Biology & Genetic Engineering Lab (BC - 332)

Year 2023-24 (Odd Semester)

  1. Fundamentals of Bioinformatics (BC - 434)
  2. Regulatory Aspects of Biotechnology (BC - 502)

Year 2022-23 (Even Semester)

  1. Molecular Biology & Genetic Engineering (BC - 332)
  2. Genetic Engineering (BC - 534)
  3. Molecular Biology & Genetic Engineering Lab (BC - 332)

Year 2022-23 (Odd Semester)

  1. Fundamentals of Bioinformatics (BC - 434)
  2. Regulatory Aspects of Biotechnology (BC - 502)

      Funding

      • SERB (SRG), India (2023-2025) in the area of protein reconstruction (Role: PI).
      • Collaborative Research Project Grants in Biotechnology, from Science and Technology Department, Govt. of Odisha (2023-2026) in the area of hypothyroidism and neurodegeneration (Role: Co-PI).
      • IIT (BHU) Institute Seed Grant (2022-2024) (Role: PI).

      Invited talks

      1. Invited talk at the FDP on "Bioinformatics and Computational Biology Approach in Present-day Research" organized by the University of Engineering and Management (UEM), Kolkata, India from 6-10 November 2023.
      2. Invited talk at the "International Conference on Structural Biology and Drug Discovery 2023", School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. from 11-12 October 2023.
      3. Expert lecture in five days FDP on "Current Trends of Natural Language Processing and Deep Learning in Bioinformatics" organized by the Department of Computer Science and Engineering, NIT Patna, from 9-13 October 2023.
      4. Extramural talk at Department of Biotechnology & Center of Excellence in Integrated OMICS and Computational Biology, Utkal University on May 25th, 2023.
      5. Faculty Development Program (FDP) on the "Development of Therapeutics using Bioinformatics: Recent Trends and Developments" by the NIT Warangal Teaching Learning Center (TLC) Under PMMMNMTT Scheme of MHRD, Govt. of India from May 8th-12th, 2023.
      6. International Webinar on “Multi-Omics approaches for sustainable Health & Agriculture” Organized by Centre of Excellence in Integrated Omics & Computational Biology, Utkal University, Bhubaneswar, India, on 21 December 2021.
      7. “Recent Trends in Structural Bioinformatics and Computer-Aided Drug Design, SBCADD’2019”, Alagappa University, Karaikudi, India, from 12-15 February 2019.
      8. Department of Biotechnology, Utkal University, Bhubaneswar, India, on 14 April 2018. 

      Key presentations

      1. Aditya K. Padhi, Ashutosh Kumar, Ken-ichi Haruna, Haruna Sato, Hiroko Tamura, Satoru Nagatoishi, Kouhei Tsumoto, Atushi Yamaguchi, Fumie Iraha, Mihoko Takahashi, Kensaku Sakamoto*, Kam Y. J. Zhang (2021) “An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes” at the RIKEN Biosystem Dynamics Research Retreat, October 28-29, 2021.
      2. Aditya K. Padhi, Ashutosh Kumar, Kensaku Sakamoto and Kam Y.J. Zhang (2020) “Computational design and experimental characterization of non-canonical amino acid coupled therapeutic nanobodies” at the 8th RIKEN Life Science Retreat (Complexity), February 6-7, 2020 (Poster presentation).
      3. Sota Yagi, Aditya K. Padhi, Kam Y. J. Zhang, Shunsuke Tagami (2020) “Reconstruction of the original core of RNA polymerase from short peptide” at JpGU-AGU Joint Meeting 2020 (Japan Geoscience Union, American Geophysical Union), July 12-15, 2020 (Oral presentation).
      4. Aditya K. Padhi, Motoi Yamashita, Ichiro Taniuchi, Kam Y.J. Zhang (2016) “Computational Investigation of the Role of AIOLOS Mutations in B-cell Deficiency and Familial Lymphoma” at Center for Life Science Technologies Retreat from 9-10 November 2016 (Poster presentation).
      5. Aditya K. Padhi, B. Jayaram, James Gomes (2014) “Residue Specific Conformational Switching and Local Folding in Human Angiogenin Mutants Cause Amyotrophic Lateral Sclerosis through Loss of Functions” at Gordon Research Conference on Protein Folding Dynamics – From the Computer to the Cell: Protein Folding, Function and Evolution at Galveston, Texas, the USA from 5-10 January 2014 (Poster presentation).
      6. Aditya K. Padhi, B. Jayaram, James Gomes (2013) “Inferring Functional Implications of Missense Angiogenin Mutations in Amyotrophic Lateral Sclerosis through Molecular Dynamics Simulations” at Bioworld2013–Computational Biology in Disease and Disorder, IIT Delhi from 9-11 December 2013 (Oral presentation).
      7. Aditya K. Padhi, Ashutosh Shukla, Saumya Verma, James Gomes, Manidipa Banerjee (2013) “Structural and dynamic commonalities among membrane-penetrating peptides of non-enveloped viruses” at Bioworld2013 – Computational Biology in Disease and Disorder, IIT Delhi from 9 – 11 December 2013 (Poster presentation).
      8. Aditya K. Padhi, B. Jayaram, James Gomes (2013) “A Molecular Dynamics Simulation-Based Prediction of Deleterious Angiogenin Mutations Causing Amyotrophic Lateral Sclerosis” at Albany 2013: Conversation 18 at the State University of New York at Albany from 11 - 15 June 2013 (both oral and poster presentations).
      9. Aditya K. Padhi, B. Jayaram, James Gomes (2013) “Angiogenin Variants D22G and V103I cause Amyotrophic Lateral Sclerosis by Loss of Functions: A Prediction Based on Molecular Dynamics Simulation Studies” at International Conference on Biomolecular Forms and Functions (ICBFF-2013) - A celebration of 50 years of the Ramachandran Map, Indian Institute of Science, Bangalore, 8 - 11 January 2013 (Poster presentation).
      10. Suhas V. Vasaikar, Aditya K. Padhi, B. Jayaram, James Gomes (2011) “NeuroDNet: a Database for Constructing and Analyzing Neurodegenerative Disease Networks.” International Symposium on Systems Biology in Physiology/Medicine, Indian J Physiol Pharmacol, Vol. 55, No. 5, Supp 2011.
      11. Suhas V. Vasaikar, Aditya K. Padhi, James Gomes (2011) “Network Analysis of Neurodegenerative Diseases: A System-based Approach to Uncover Perturbed Networks.” Front. Neuroinform. Conference. 4th INCF Congress of Neuroinformatics Boston.
      12. Aditya K. Padhi, Suhas V. Vasaikar, Hirdesh Kumar, James Gomes (2011). “Molecular dynamics simulation study of human angiogenin variants implicated in Amyotrophic Lateral Sclerosis” at 25th Annual Meeting of Society for Neurochemistry, India (SNCI) and International Symposium on Metabolic Signalling in Brain in Health and Diseases, University of Hyderabad, Hyderabad, India from 7-9 January 2011 (Poster presentation).

      Administrative Responsibilities & Services

      • Senate Member: Indian Institute of Technology (BHU) Varanasi from April 2023 - Present.
      • Organizing Secretary: Short-term course on Advanced Functional Materials and Informatics (AFMI-2023) from 29 November - 03 December 2023, at IIT (BHU) Varanasi (I-DAPT-Hub supported).
      • Convenor: Departmental Library Convenor, 2023 (School of Biochemical Engineering).
      • Member: Departmental Purchase Committee, FY 2023-24
      • Member: M.Tech. Admission Committee 2022 & 2023 (School of Biochemical Engineering).
      • Member: Ph.D. Admission Committee 2022 & 2023 (School of Biochemical Engineering).
      • Member: Department Postgraduate Committee (DPGC) for session 2022-23 (School of Biochemical Engineering).
      • Organizing Secretary: Short-term course on Computer-Aided Drug Design and Structural Bioinformatics (CADDSB-2023) from March 13-17, 2023, at IIT (BHU) Varanasi (I-DAPT-Hub supported).
      • Organizing Committee Member: For the I-DAPT HEALTH-TECH HACKATHON, IIT (BHU), Varanasi (July 2022).

      Opportunities

      Motivated project fellows, Ph.D. students, and postdoctoral fellows interested in joining our laboratory are encouraged to contact Dr. Aditya Kumar Padhi by email.

      Candidates having prior experience in computational biology/biophysics, structural bioinformatics, biomolecular simulations, and programming skills are desirable but not mandatory.

      Please send your CV to (aditya.bce@iitbhu.ac.in) with a brief description of your research interests and what you would like to work in the broad areas of computational biology (following institute norms).

      Contact

      Dr. Aditya Kumar Padhi
      Assistant Professor
      Laboratory for Computational Biology & Biomolecular Design,
      School of Biochemical Engineering
      Indian Institute of Technology (BHU) Varanasi
      Varanasi 221005, Uttar Pradesh, India
      Email: aditya.bce@iitbhu.ac.in & dradityapadhi@gmail.com