Neeladri Sen

Experience

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  Indian Institute of Science Education and Research (IISER), Pune

  Aug 2015 - Sept 2020

  Graduate Research Fellow

  Ph.D. researcher with Prof. M. S. Madhusudhan, IISER Pune, India 2015-2020Thesis - Characterizing protein surfaces for binding associations Creation of a database of protein-protein/domain-domain interface and associated ligand binding sites, which could be targeted by ligands to disrupt these interactions. (https://doi.org/10.1002/pro.4406) Prediction and modeling of coiled-coil protein-protein interface. Development of a statistical potential to predict interface residues based on physico-chemical properties of known interfaces. Development of tools to identify interface residues which on mutation would impact the binding more (referred to as hotspot residues), based on conservation and physico-chemical properties. Prediction of off-target binding partner of Nutlin (a molecule which is currently under trails for cancer) on other human proteins based on structural similarity of binding pockets. This was followed by various physico-chemical and binding energy calculations. (https://doi.org/10.1021/acs.jcim.8b00762) Modelling of Nipah proteome, predicting and designing therapeutics against them. Studying the stability of the therapeutic-viral proteins and effect of viral mutations. (https://doi.org/10.1371/journal.pntd.0007419) Studying microenvironments in protein structure to develop a tool to predict effect of mutations. (https://doi.org/10.1016/j.pbiomolbio.2017.02.004) Show less

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  Birkbeck, University of London

  Sept 2017 - Dec 2017

  Newton Bhabha exchange PhD Scholar

  Exchange PhD scholar to work with Prof. Maya Topf at Birkbeck to develop statistical potentials to score protein-protein interfaces

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  UCL

  Apr 2020 - Mar 2025

  Postdoctoral Researcher

  Post-doctoral researcher with Prof. Christine Orengo, UCL, UK 2020-onwards Identification of function determining residues in the triterpene synthase family of proteins (a protein family that uses a single substrate to produce hundreds of products). Explanation of enzymatic pathway for formation of different products based on binding pocket characteristics, binding energies, molecular dynamic simulations etc. Characterization and explanation of the impact of disease associated mutations in human proteins without known structures or structural homologues. This was done based on proximity to functional sites, structural destabilization and pathogenicity. (https://doi.org/10.1093/bib/bbac187) Development of tools to predict functional sites in proteins using machine learning & deep learning. (https://doi.org/10.1093/bioinformatics/btaa937) Analysis of superfamilies in the CATH database to identify conserved sequential/structural motifs to explain the functioning of protein families eg. HUPs superfamily. (https://doi.org/10.1101/2023.10.12.562014) Study the AlphaFold models with special importance to plant stress related proteins, to explain how plants deal with stress. Examination of the SARS-CoV2 viral and interacting host protein to examine the effect of mutations in both the virus and host. (https://doi.org/10.1038/s41598-024-61541-1) Development of a nextflow pipeline to predict the impact of mutations Show less

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  DIOSynVax

  Apr 2025 - now

  Senior Bioinformatician

  Design and Development of vaccines