DEBARATI PAUL

Ph.D. (Thesis submitted) in Biophysics, Molecular Biology and Bioinformatics, University of Calcutta (Worked at Bose Institute), Kolkata Thesis: “Mechanistic Insight Into The Intrinsic Dynamics Of Bcl-2 Proteins And Dissecting The Influences Of The Disordered And Ordered Regions On Their Regulation” Supervisor: Prof. Shubhra Ghosh Dastidar, Department of Biological Sciences, Bose Institute, Kolkata Brief synopsis of the PhD works: Functional regulation of Bcl-2 proteins as a result of modification has disease consequences. Perturbation in the interactions at molecular level underlie functional alteration. The investigations in my PhD thesis were expounded upon the molecular mechanism to delineate how modifications like mutation and phosphorylation in the highly conserved and ordered region and the diverse disordered regions of anti-apoptotic Bcl-2 proteins affect their inherent dynamics, leading to perturbation in intra as well as intermolecular interactions. By providing all-atom description, the works aimed to provide a comprehensive understanding of the altered interactions, thus facilitating rational drug discovery processes. Key proteins under investigations included Bcl-2, Bcl-xL, and Beclin1. 2020-2023: Senior Research Fellow at Bose Institute 2018-2020: Junior Research Fellow at Bose Institute Skillset: Methods in computational biology including Molecular Dynamics, molecular modelling using various Bioinformatics approaches, Docking, Virtual screening, Data analysis, Performing calculations in Computer Clusters, Management of HPC systems, Linux OS, Programming with R, Shell, CHARMM scripting. Proficient in using packages like CHARMM, NAMD, Gromacs, Schrodinger, Autodock and various others in CPU and GPU based platforms. Outgoing student pursuing flexible part-time employment with weekend and evening shift options.

• Oral, Mechanistic insight into the influence of the disordered region of bcl-2 protein on its function, SBC, 04/2021
• Oral, Multi-conformation representation of COVID-19 Mpro identifies promising candidates for drug repurposing, BIC Webinar, 06/2021
• Poster, IDR Modification of Anti-Apoptotic Bcl-2 Proteins Reshape Their Binding Pocket Dynamics, Debarati Paul, Prerna Priya, Shubhra Ghosh Dastidar, ICDD, 03/2020
• Poster, Finding antivirals using ensemble based virtual screening approach, Debarati Paul, Debadrita Basu and Shubhra Ghosh Dastidar, ICDD, 11/2022
• Poster, Molecular Dynamics Elucidates the Route to Transmit Decisive Molecular Messages from IDR to the Site of Function of Bcl-2, Debarati Paul, Premananda Basak, Shubhra Ghosh Dastidar, SBC, 12/2022

Methods in computational biology including Molecular Dynamics, molecular modelling using various Bioinformatics approaches, Docking, Virtual screening, Data analysis, Performing calculations in Computer Clusters, Management of HPC systems, Linux OS, Programming with R, Shell, CHARMM scripting. Proficient in using packages like CHARMM, NAMD, Gromacs, Schrodinger, Autodock and various others in CPU and GPU based platforms.

Ph.D., Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Bose Institute, Kolkata, WB, Mechanistic Insight Into The Intrinsic Dynamics Of Bcl-2 Proteins And Dissecting The Influences Of The Disordered And Ordered Regions On Their Regulation, Prof. Shubhra Ghosh Dastidar, Department of Biological Sciences, Bose Institute, Kolkata

• Remote communication between unstructured and structured regions of Bcl-2 tunes its ligand binding capacity: Mechanistic insights, Paul D, Basak P & Ghosh Dastidar S, CBAC, 2022
• Multi-conformation representation of Mpro identifies promising candidates for drug repurposing against COVID-19, Paul D, Basu D & Ghosh Dastidar S, JMM, 2021
• In silico analyses of Wnt1 nsSNPs reveal structurally destabilizing variants, altered interactions with Frizzled receptors and its deregulation in tumorigenesis, Mondal A, Paul D, Ghosh Dastidar S, Saha T & Goswami AM, Scientific Reports, 2022
• Modeling and monitoring the effects of three partly conserved Ile residues in the dimerization domain of a Mip-like virulence factor from Escherichia coli, Seal S, Chakraborty T, Polley S, Paul D, Banerjee N, Sinha D, Dutta A, Chatterjee S, Sau K, Ghosh Dastidar S & Sau S, JBSD, 2023
• A novel acidic pH-dependent metacaspase governs defense-response against pathogens in tomato, Basak S, Paul D, Das R, Ghosh Dastidar S & Kundu P, PPB, 2024

• In silico drug design and molecular dynamics simulations, Cytogene, 12/2021
• Cheminformatics and machine learning in drug discovery for beginners, NyBerMan Bioinformatics, 09/2023