Dr. Aditya Kumar Padhi
Assistant Professor
School of Biochemical Engineering IIT(BHU)
aditya.bce@iitbhu.ac.in
.
Area of Interest:
Computational Biology, Structural Bioinformatics, Computational Biophysics, High-throughput Protein Design, Translational Bioinformatics, Biomolecular Modeling and Conformational Analyses
- Profile
- Publications
- Awards & Honors
- Professional Membership & Services
- Research Interest
- Teaching
- Invited Talks & Key Presentations
- Administrative Responsibilities
- Contact & Opportunities
Education
Ph.D., Indian Institute of Technology Delhi, India
Computational Biology
B.Tech., Biju Patnaik University of Technology, 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: 780+; h-index: 14; i10-index: 19 (*Corresponding author)
Peer-reviewed journal articles
37. 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, [published online ahead of print, 2022 Sep 7]. 2022;629:54-60. doi:10.1016/j.bbrc.2022.09.010 (IF: 3.322).
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36. 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, elac020, https://doi.org/10.1093/bfgp/elac020 (IF: 4.840).
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35. 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).
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36. 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, elac020, https://doi.org/10.1093/bfgp/elac020 (IF: 4.840).
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35. 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).
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34. 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].
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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).
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34. 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].
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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).
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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).
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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).
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:
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).
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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).
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).
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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).
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).
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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).
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:
Tokyo Medical and Dental University: https://www.tmd.ac.jp/pressrelease/202100621_1/
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26. Aditya K. Padhi, Soumya Lipsa Rath, and Timir Tripathi (2021) Accelerating COVID-19 Research Using Molecular Dynamics Simulation, The Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.1c04556 (IF: 3.466). [This article has been selected for the cover page of JPCB, issue 33 (dated 8/26/21)].
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26. Aditya K. Padhi, Soumya Lipsa Rath, and Timir Tripathi (2021) Accelerating COVID-19 Research Using Molecular Dynamics Simulation, The Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.1c04556 (IF: 3.466). [This article has been selected for the cover page of JPCB, issue 33 (dated 8/26/21)].
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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).
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).
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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). [This article is among the top 25% of most-cited PLoS ONE articles].
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). [This article is 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.
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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.
Awards & Honors
- Selected as a Postdoctoral Fellow (top 50 candidates worldwide) for IndiaBioscience’s PDF Meeting 2021.
- Selected as a Postdoctoral Fellow (top 50 candidates worldwide) for IndiaBioscience’s 13th Young Investigator Meeting 2021.
- Tokyo Biochemical Research Foundation (TBRF) International Fellowship Program – 2019 for conducting research in Japan.
- Takeda Science Foundation International Fellowship Program – 2019 for conducting research in Japan (Awarded but Not Availed).
- Japan Society for Promotion of Science (JSPS) Postdoctoral Research Fellowship – 2017 for conducting research in Japan.
- 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.
- “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).
- 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).
- 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).
- 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).
- Senior Research Fellowship (SRF) from the Council of Scientific & Industrial Research (CSIR), New Delhi, India (2013 – 2016) for doctoral studies.
- 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
- Life member of Biophysical Society, Rockville, Maryland, USA.
- Life member of Indian Biophysical Society (IBS), India.
- Life member of Bioinformatics and Drug Discovery Society (BIDDS), India.
- American Association for Advancement of Science (AAAS).
- Life member of Society of Neurochemistry (SNCI), India.
- Life member of Association of Biotechnology Led Enterprises (ABLE), India.
Editor & Reviewer for Journals
- Review Editor: Frontiers in Molecular Biosciences, Structural Biology Section.
- Wiley: (1) Protein Science; (2) Journal of Cellular Biochemistry
- Oxford University Press: (1) Briefings in Bioinformatics, (2) Briefings in Functional Genomics
- American Chemical Society: (1) ACS Omega
- Elsevier: (1) International Journal of Biological Macromolecules; (2) Computational and Structural Biotechnology Journal; (3) Drug Discovery Today; (4) Computers in Biology and Medicine; (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
- 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 analysis of disease-causing genetic variations, SNPs, rare variants, and conformational analysis 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.
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 analysis of disease-causing genetic variations, SNPs, rare variants, and conformational analysis 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.
Year 2022-23 (Odd Semester)
- Fundamentals of Bioinformatics (BC434)
- Regulatory Aspects of Biotechnology (BC502)
Invited talks
- 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.
- “Recent Trends in Structural Bioinformatics and Computer-Aided Drug Design, SBCADD’2019”, Alagappa University, Karaikudi, India, from 12-15 February 2019.
- Department of Biotechnology, Utkal University, Bhubaneswar, India on 14 April 2018.
Key presentations
- 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.----
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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).
- 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.
- 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.
- 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).
- Member, Department Postgraduate Committee (DPGC), for session 2022-23.
- Organizing Committee Member, I-DAPT HEALTH-TECH HACKATHON, IIT (BHU) Varanasi (July, 2022).
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
Opportunities
Highly motivated students, 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. 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).
