Hridoy Ranjan Bairagya, Ph.D
hridoy.bairagya[at]makaut[dot]ac[dot]in
Professional Experience:
Associate Professor, Department of Bio-informatics, Maulana Abul Kalam Azad University of Technology, Haringhata, Nadia, 741249, West Bengal (2022 to date).
Assistant Professor, Department of Bio-informatics, Maulana Abul Kalam Azad University of Technology, Haringhata, Nadia, 741249, West Bengal (2021 to 2022).
Visiting Faculty (Assistant Professor) in M.Sc. Bioinformatics at Department of Computer Science in Central University, Jamia Millia Islamia -New Delhi, from 2018 to 2020.
Research Associate at Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India in the group of Prof. T.P.Singh. (2020 to 2021).
CSIR-Scientist Pool (Council of Scientific and Industrial Research, Govt. of India) at Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. India in the group of Prof. T.P.Singh. (2017 to 2020).
Research Associate (funded by European Research Council) at Department of Chemistry, University of Cambridge, UK in the group of Prof. David J. Wales. (2015 to 2016).
Young Scientist/PI (funded by of Science and Engineering Research Board, Govt. of India) at Molecular Biophysics Unit, Indian Institute of Science-Bangalore, India in the group of Prof. Manju Bansal (2013 to 2015).
Post Ph.D. Research Fellow at Department of Chemistry, National Institute of Technology –Durgapur, India in the group of Prof. Bishnu Prasad Mukhopadhyay (2012 to 2013).
Education:
Ph.D. in Engineering in Biotechnology (specialization “Bioinformatics”) from National Institute of Technology-Durgapur, Govt. of India, 2012.
Teaching Experience:
Course:
M.Tech. Bioinformatics
M.Sc. Bioinformatics
B.Sc. Bioinformatics
Subjects Taught: Applied Biochemistry , Protein Engineering , Bio Molecular Dynamics , Drug Design, Computational Biochemistry , Structural Bioinformatics , Molecular Modeling and Molecular Dynamics, and Computational Drug Design , Computational Biology.
Awards:
Research Award of Excellence in the field of research during the 4th International Conference on Environmental, Agricultural, Chemical, and Biological Sciences #ICEACBS2023 in support of United Nations SDGs from Voice of Indian Concern for the Environment (VOICE), Department of Biotechnology, Srimad Andavan Arts and Science College, Trichy,Tamilnadu, India, Somnogen Canada Inc., Toronto, Canada, All India Institute of Training and Education (AIITE), New Delhi, India during May 13-14, 2023.
Best Oral presentation award from 4th International Conference on Environmental, Agricultural, Chemical and Biological Sciences, ICEACBS 2023, Department of Biotechnology, Srimad Andavan Arts and Science College, Trichy, Tamilnadu, India, Department of Studies in Biotechnology, Vijayanagar Sri Krishnadevarya University, Ballari, Karnataka. May 13-14, 2023.
Received award on Health Science from Sustainability Carnival” at PRME (United National Global Company)-IILM Academy of Higher Learning, Greater Noida on 14-15 February 2020.
International Research Project: The research proposal “Novel application of energy landscapes methodology to analyze conformational transitions and binding pathways of HIV-I TAR-RNA with TAT protein and other potential inhibitors” submitted under Marie Skłodowska-Curie actions fellowship (2016), was scored as a high-quality project proposal in a highly competitive evaluation process. This proposal is recommended for funding by other sources since Horizon 2020 resources.
Received Foreign travel Grant from C.S.I.R., Govt. of India on 2009.
Received Foreign travel Grant from C.S.I.R., Govt. of India on 2011.
Bruker Axs India Best Poster Award: In 2008, “37th National Seminar on Crystallography “, held at Jadavpur university one of our research work “Invariant Water Molecular Dynamics at the catalytic site of IMPDH II “Bruker Axs India Best
Poster Award:
Received award from Institute Research Fellowship from National Institute of Technology –Durgapur, Govt. of India, for the period 2006 – 2010.
Received award from the Council of Scientific and Industrial Research (CSIR, Govt. of India), Senior Research Fellowship for the period 2010.
Recipient of a “Young Scientist” award from Science and Engineering Research Board (Govt. of India), 2013.
Received award from the Council of Scientific and Industrial Research (CSIR, Govt. of India), Senior Research Associateship (Scientist’s Pool scheme) for the period 2017.
Research Interests:
Cancer Bioinformatics
Research Methodology
Computational Chemistry: MD simulation study of proteins, enzyme–substrate complexes, protein-metal complexes and RNA-peptide complexes. pH dependent MD simulation study of enzyme to mimic experimental methods. Water molecular dynamics of macromolecules. Identification of hydration or water sites in protein using Inhomogeneous Fluid Solvation theory (IFST). thermodynamic and structural dynamic parameters of water molecules and analysis of their correlation. Conformational dynamics of RNA-peptide complexes. Loop-flap molecular dynamics study of protein. Binding free energy calculation of ligand by MM (GB) PB and LIE-D methods. Thermal denaturation of ribozyme. Force filed parameterization of new ligands.
Computational Drug Discovery: Salt Bridge based drug discovery. Conserved water based drug discovery using Inhomogeneous Fluid Solvation theory (IFST). Isoform specific drug discovery, Structure based drug discovery, Enzymatic mechanism based drug discovery. Virtual screening from ligand database, QSAR and ADMET Properties Prediction. Statistical analysis for drug discovery.
Computational Biophysics: Protein engineering, Prediction of 3D structure of protein and loop of the protein structure by homology modeling, energy minimization and molecular dynamics simulation study. Modeling the ternary complexe of metallo proteins. Inter domain recognition process of macromolecules. Identifying and modeling the key water molecules in protein and protein-ligand complexes. Prediction the flexibility and functional role of water molecules. Methods for pocket monitoring during MD simulation.
Structure Refinement and Protein Crystallography: Structure prediction of protein and protein-ligand complexes using molecular replacement method. **Protein structures (PDB Id: 6LSO, 5YL8, 5ZZV, 6A31, 6JJQ, 5YRR, 6JOG, 6IDM, 6A89, 5YIH) deposited at Protein Data Bank.
Computational Biochemistry: Purine nucleotide biosynthesis pathway analysis. Activity and mechanism of enzyme. Conformational transition of enzyme from ligand free to ligand bound state. Prediction the functional role of non catalytic residues of enzyme – substrate complexes. Identification of allosteric site of the enzyme. Subsite site recognition of ligands.
Molecular Modeling and Docking study: Prediction the model structure of new ligand and modification of existing ligand on the basis of ligand–water interaction. Database development of new ligands. Molecular docking study of protein-protein, protein-inhibitor, protein-ligand and protein-drugs.
**Interested on Disease: Blood cancer (Chronic myeloid leukemia (CML) caner), TTR (Transthyretin) associated amyloid diseases, arthritis and Viral disease (Covid-19)
Lab Members:
Present :
Ph.D. Student:
Dipesh Chakraborty, Ph.D. Fellow (Assistant Professor, Department of Pharmaceutical Science & Technology, Co-PI: Dr. H.R. Bairagya).
Research Project Trainee (2024):
Kirtiman Mahata (Project Trainee, M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB ).
Manti Biswas (Project Trainee, M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB ).
Shrestha Sengupta(Project Trainee, M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB ).
Deotima Chakraborty (Project Trainee, M.Tech Bioinformatics, Department ofBioinformatics,MAKAUT,WB ).
Alumni Lab Members:
Sayanti Pal (M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB,2023 ).
Swapnil Pal (M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB,2023).
Moumita Mohanta (M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB ,2023).
Rudra Nath Banerjee (M.Tech Bioinformatics, Department of Bioinformatics, MAKAUT,WB ,2023).
Anubha Kar (M.Sc. Bioinformatics, Department of Bioinformatics, MAKAUT,WB ,2023).
Sweety Gupta (M.Pharm, Department of Pharmaceutical Science and Technology, MAKAUT,WB ,2023).
Zinnat Akter Zahan (M.Pharm, Department of Pharmaceutical Science and Technology, MAKAUT,WB,2023 ).
Subham Sen (M.Sc. in Genetics, Department of Pharmaceutical Science and Technology, MAKAUT,WB ,2023).
Sourav Sarkar (M.Sc. in Genetics, Department of Pharmaceutical Science and Technology, MAKAUT,WB,2023 ).
Saheli Majumder (Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, WB,2023 ).
Debapriyo Sarmadhikari (Department of Bioinformatics, M.Tech-Bioinformatics, MAKAUT, 2022). Thesis Title: “Investigate the role of conserved water molecules in the catalytic domain of the Mpro protein: A study by Molecular Dynamics Simulation”
Saborno Boral (Department of Bioinformatics, M.Tech-Bioinformatics, MAKAUT, WB,. 2022). Thesis Title: “Identification of conserved water molecules and repurposing of Drugs of human GRK2 Protein: A study by structural Bioinformatics method”
Archita Bhattacherjee (Department of Bioinformatics, M.Tech-Bioinformatics, MAKAUT,2022). Thesis Title: “A Comparative Study of Water molecule and Salt Bridge between human GMPS and non human GMPS Protein: A Study by Structural Bioinformatics Method”
Riddhe Rakshit (M.Sc. Molecular Biology, MAKAUT, 2022). Thesis Title: “Effect of CML cancer Drug on "human Inosine Monophosphate Dehydrogenase –I": A Structural Bioinformatics Study”
Anushree Dutta (M.Sc. Molecular Biology, MAKAUT, 2022). Thesis Title: “Repurpose of Drug for CML Cancer Protein -" human Tyrosine Kinase": A Study by Computational Drug Discovery Method”
Swagata Das (M.Sc. Molecular Biology, MAKAUT, 2022). Thesis Title: “Repurpose of CML cancer Drug for "human Inosine Monophosphate Dehydrogenase –II": An approach by molecular docking method”
Projects Running:
Research Project ( Recommended ) to Department of Biotechnology (Govt. of India) in the area of Bio-Molecular Simulation.
Proposed Project Title: “Investigation of the Structural, Dynamical, and Biochemical Mechanism in Human Guanosine Monophosphate Reductase (hGMPR) Enzyme: A Study towards the Design of Anticancer Agent”.
(Total Proposed Budget: Rs. 34, 50000/-)
Projects Completed:
Project Title: “Molecular dynamic simulation study on human guanosine monophosphate synthetase(GMPS) enzyme and their hydrated complex: A theoretical approach towards the design of anticancer agent”.
Host Institute: Molecular Biophysics Unit, Indian Institute of Science-Bangalore, PIN-560 012.
Sponsoring Agency: Science and Engineering Research Board, D.S.T., Govt. of India.
Purpose of the award: It was instituted to provide research funding to the “Young Scientist” below the age of 35 years to undertake independent research in newly emerging and frontier areas of Science and Engineering.
Nature of Award: A total research grant of Rs. 18 lakhs for a period of three Years.
Invited Scientific Talk/ Oral Presentation:
Speaker of International Conference (Online) “New Biochemical Insights of Conserved Water Molecules in SARS-CoV-2 Main Protease: A Future Hope for Discover of anti-Covid Molecule”. 4th International Conference on Environmental, Agricultural, Chemical and Biological Sciences , ICEACBS 2023, Department of Biotechnology, Srimad Andavan Arts and Science College, Trichy, Tamilnadu, India, Department of Studies in Biotechnology, Vijayanagar Sri Krishnadevarya University, Ballari, Karnataka. May 13-14, 2023,
· Speaker of International Conference (Online) on “Bioinformatics and its Application” dated 21th to 22nd December,, 2022 at the Shree Ukabhai Dodiya P.G.Center and Shree Mahila Arts and Science College, Simar, Gujarat. Scientific talk entitle “Application of Bioinformatics in the area of Molecular Modelling”.
Speaker of International Conference (Online) on “Biomolecules to Biome (BMB)” dated 24th to 25th August 2022 at the Department of Life Sciences, Presidency University, Kolkata. Scientific talk entitle “New Biochemical Insights into the Dynamics of Conserved Water Molecules at the substrate binding site of the human GMPR Enzyme”.
Speaker and resource person of Faculty Development Program on " Computational Approach to Molecular Docking and Drug Designing and Its Scope in the Entrepreneurial World” dated on 29th July, 2022 at Department of Biotechnology, Haldia Institute of Technology (MAKAUT). Scientific talk "Role of Conserved Water Molecules in Computational Drug Discovery". https://www.youtube.com/watch?v=MkAZSheYNyc at YouTube.
Speaker and resource person of Faculty Development Program on "Computer Science and Biology: Impact of Bioinformatics and Molecular Biology on Drug Discovery” dated on 7th October, 2021 at Department of Biotechnology, IILM, University-Greater Noida – 201306. Scientific talk "Biomolecular Simulations in Computer‐Based Drug Discovery".
Invited as an expert and resource person of summer school “Bioescalator: Insights into Biotechnology, Plant Science and Bioinformatics” on 22ndMay, 2020 at Department of Biotechnology, IILM University- Greater Noida, New Delhi and delivered the scientific talk on “MD Simulations & its application in drug discovery”. The scientific talk is available https://www.youtube.com/watch?v=zmDyYOj4sBM at YouTube.
Speaker and resource person on National Seminar of “Recent Trends in Pharma Biotechnology” at Department of Biotechnology, IILM College of Engineering & Technology, Greater Noida, UP on September 17th, 2019.
Keynote Speaker (Title: “New insights into the dynamics of enzyme and nucleic acids: Computational approaches for conserved water based drug discovery”) at National Workshop (9th) on Translational Bioinformatics at Department of Computer Science, Jamia Millia Islamia, New Delhi from 6th March to 7th March, 2019.
Speaker and resource person of the program "Approaches for In silico drug designing" sponsored by A.P.J. Abdul Kalam Technical University, on July 3-7, 2018 at Department of Biotechnology at IILM College of Engineering & Technology, Greater Noida, UP.
Deliver the invited scientific talk on “New insights into the dynamics of enzyme and nucleic acids: Computational approaches for conserved water based drug discovery” at Department of Biotechnology, Siksha, Bhavana, Visva-Bharati University (Santiniketan-731235) dated on 6th March, 2017.
Delivered the scientific talk at Albany, USA in the “The 17th Conversation “on June 14-18, 2011, State university of New York, USA in the Young Scientists Speaker Program.
Deliver Scientific talk at 40th National Seminar on Crystallography–2011 (Osmania University, Hydrabad, India) dated 23rd – 25th October, 2011.
International Book Publications :
Hridoy R. Bairagya*, Archita Bhattacharjee, and Sabarno Baral,
"NEW STRUCTURAL INSIGHT OF HUMAN GMP SYNTHETASE ENZYME: Computational Study for Drug Repurpose in Chronic Myeloid Leukemia” ELIVA press SRL(ISBN: 978-9994981427) Europe, Page:1-106, 2022.* [as Corresponding author].
Hridoy R. Bairagya*, Gyan Prakash Rai, Alvea Tasneem, and Saima Reyaz
“A New Approach for Understanding the Mechanism and Drug Design of Chronic Myeloid Leukemia Responsive Protein” ELIVA press SRL(ISBN: 978-1952751516) Europe, Page:1-48, 2020.
* [as Corresponding author].
Publications (Peer reviewed Articles): Google scholar link https://scholar.google.co.in/citations?user=vMyhsZkAAAAJ&hl=en
[Total publications: 44, **Total Citations: 379, h-index:13 and i10-index:18]
“Publication as Corresponding author”
Hridoy R. Bairagya*, AlveaTasneem, and Debapriyo Sarmadhikari
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory, Proteins: Structure, Function, and Bioinformatics. 2024. *[Corresponding author]
Hridoy R. Bairagya*, Sweety Gupta, and Sayanti Pal
International Journal of Bioinformatics and Intelligent Computing 3 (1), 70-90, 2024. *[Corresponding author]
A Tasneem, A Sultan, P Singh, Hridoy R. Bairagya, H Almasoudi, AYM Alhazmi, ...
Identification of potential therapeutic targets for COVID-19 through structural-based similarity approach between SARS-CoV-2 and its human host proteins.Frontiers in Genetics 15, 1292280, 2024.
Hridoy R. Bairagya*, Sayanti Pal
A Bioinformatics Approach to the Identification of Conserved and Semi-Conserved Water Molecules in Kinase Domain of hGRK2 Protein. JSM Enzymology and Protein Science 1012 (4 (1)), 1-8, 2023.*[Corresponding author]
Hridoy R. Bairagya*, Sweety Gupta, and Sayanti Pal
Investigation of Structural Analogues of Azithromycin and Remdesivir for SARS-CoV-2 Mpro: A Computational Approach in Drug Development. Journal of Pharmacology and Clinical Toxicology 11 (2), 1-12, 2023.*[Corresponding author]
Hridoy R. Bairagya*, Sweety Gupta
Conformational Transition from Native to Ligand Bound State of Mpro enzyme: A Study by Computational Method.International journal of recent advances in Biotechnology. (2023).*[Corresponding author]
Hridoy R. Bairagya*, Alvea Tasneem, Gyan Prakash Rai, and Saima Reya
Structural and Dynamical Impact of Water Molecules at Substrate or Product Binding Site in Human GMPR Enzyme: A Study by MD Simulation. ACS-Journal of Physical Chemistry-B,
DOI: 10.1021/acs.jpcb.0c08818, 125(5), 1307-1530, 2021. *[Corresponding author]
**Research work cited at Cover or Front Page of the ACS-Journal.
Hridoy R. Bairagya*, Alvea Tasneem, Gyan Prakash Rai, Saima Reyaz
New Biochemical Insights into the Dynamics of Water Molecules at GMP or IMP binding Site of human GMPR Enzyme: A Study by MD-Simulation. Proteins: Structure, function and Bioinformatics, 90 (1), 200-217, 2021. *[Corresponding author]
Saima Reyaz, Alvea Tasneem, Gyan Prakash Rai, and Hridoy R. Bairagya*
Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study. Journal of Molecular Graphics and Modeling, 109, 108021 (1-12) 2021 *[Corresponding author]
Alvea Tasneem, Gyan Prakash Rai, Saima Reyaz, and Hridoy R. Bairagya*
Role of His163, Tyr161 and Conserved Water molecules in Stabilization of Cys145-His41 Catalytic Dyad: New Insight into a possible mechanism of Main Protease in novel Coronavirus-2. SciMedicine Journal, 2,108-126, 2020.
[*Corresponding author]
Hridoy R. Bairagya*
Conformational Transition of Catalytic Domain in hGMPR enzyme from Native to Ligand Bound State: A MD Simulation Study. J. Biomolecular Structure & Dynamics, 37, 66-67, 2019. *[Corresponding author]
Hridoy R. Bairagya*, Alvea Tasneem, Gyan Prakash Rai, and Saima Reyaz.
Role of conserved water molecules at GMP binding domain in native conformation of human GMPR enzyme: A MD simulation study. Proceedings at National Workshop (9th) on Translational Bioinformatics, 2019. *[Corresponding author]
Hridoy R. Bairagya* and Manju Bansal
New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-Simulation Study. Proteins: Structure Function and Bioinformatics, 84, 360–373, 2016. *[Corresponding author]
“Publication as 1st author “
Hridoy R. Bairagya, Deepak K. Mishra, Bishnu P. Mukhopadhyay*, and K. Sekar
Conserved water-mediated recognition and dynamics of NAD+ (carboxamide group) to
hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor
J. Biomolecular Structure & Dynamics, 32(8), 1248-1262, 2014.
Hridoy R Bairagya and Bishnu P Mukhopadhyay*
Protein folding: challenge to chemistry.
J. Biomolecular Structure & Dynamics, 31(9), 993-994, 2014.
Hridoy R Bairagya and Bishnu P Mukhopadhyay*
An Insight to the Dynamics of Conserved Water Mediated Salt Bridge Interaction and Inter-Domain Recognition in hIMPDH Isoforms. J. Biomolecular Structure & Dynamics, 31(7), 788-808, 2013.
**Cited in Proteopedia as Interactive 3D Complements from Weizmann Institute of Science, Israel.
Hridoy R Bairagya, Bishnu P Mukhopadhyay*, and Asim K Bera
Role of Salt bridge Dynamics in inter domain recognition of Human IMPDH Isoforms: An Insight to inhibitorTopology for isoform –II. J. Biomolecular Structure & Dynamics. 29, 441-462, 2011.
Hridoy R Bairagya, Bishnu P Mukhopadhyay*, Payel Mallik, and Archana K. Srivastava
Conserved Water Mediated H-bonding Dynamics of Carboxamide group in NAD+ to Catalytic Asp 274 and His 93 in Human IMPDH J. Biomolecular Structure & Dynamics, 28,1008-1010, 2011.
Hridoy R Bairagya, Bishnu P Mukhopadhyay, * and Asim K Bera
Conserved Water Mediated Recognition and the Dynamics of Active site Cys 331 and Tyr 411 in Hydrated Structure of Human IMPDH-II. Journal of Molecular Recognition, 35 - 44, 24, 2011.
Hridoy R Bairagya, Bishnu P Mukhopadhyay,* and K. Sekar
An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II
(Human): Recognition of Cofactor and Substrate to Catalytic Arg 322.
J. Biomolecular Structure & Dynamics 27, 2, 149 – 158, 2009.
Hridoy R Bairagya, Bishnu P Mukhopadhyay,* and S. Bhattacharjee
Role of the conserved water molecules in the binding of inhibitor to IMPDH-II
(human): A study on the water mimic inhibitor design .
Journal of Molecular Structure:THEOCHEM 31-39, 908, 2009.
Hridoy R Bairagya and Bishnu P Mukhopadhyay*
Conserved Water Mediated Inter-Domain Recognition in IMPDH-II (human).
The 16th Conversation: at the State University of New York, Albany ,
J. Biomolecular Structure & Dynamics 26: 855, 2009.
Hridoy R Bairagya, Bishnu P Mukhopadhyay,* and K. Sekar
Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II.
J. Biomolecular Structure & Dynamics, 26,4, 497-508, 2009.
“Publication as co-author”
Sanchita Banerjee, Ankit Roy, M S Madhusudhan, Hridoy R Bairagya, and Amit Roy*
Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. Journal of Computational Biology and Chemistry 82, 65-73, 2019.
Varun Kumar, P. Sharma, H.R. Bairagya, S, Sharma, T P Singh, and Purnima Kaul Tiku,
Inhibition of human 3-hydroxy-3-methylglutaryl CoA reductase by peptides leading to cholesterol homeostasis through SREBP2 pathway in HepG2 cells. BBA - Proteins and Proteomics, 1867, 604-615, 2019.
A.Gupta, P.K.Singh, N.Iqbal, P.Sharma, H.R.Baraigya, P.Kaur, M.S.Umar, F.Ahmad, A.Sharma, M.Owais, S. harma, and T.P.Singh*
Structural and binding studies of Phosphopantetheine adenylyl transferase from A. baumannii with citric and ascorbic acid. BBA - Proteins and Proteomics, 1867 (6), 537-547, 2019.
P. Dey, Hridoy R Bairagya, and Amit Roy*
Putative role of invariant water molecules in the X-ray structures of family G fungal endoxylanases
Journal of Biosciences, 43 (2), 339-349, 2018.
A. Chaudhary, V Kumar, P. K. Singh, P. Sharm, Hridoy R. Bairagyaa, P. Kaur, S. Sharma, S. S. Chauhan, and T. P. Singh*
A glycoprotein from mammary gland secreted during involution promotes apoptosis: Structural and biological studies. Archives of Biochemistry and Biophysics, 644,72-80, 2018.
Prashant K. Singh, Naseer Iqbal, Harsh V.Sirohi, Hridoy R.Bairagya, Punit Kaur, Sujata Sharma, and Tej P.Singh*. Structural basis of activation of mammalian heme peroxidases. Progress in Biophysics and Molecular Biology, 133,4 9-55, 2018.
B. Chakrabarti, Hridoy R. Bairagya, Bishnu P Mukhopadhyay,* and K.Sekar
New biochemical insight of conserved water molecules at catalytic and structural Zn+2 ions in Human Matrix Metalloproteinase-I: A Study by MD-Simulation. Journal of Molecular Modelling, 23(2): 57,
1-13, 2017.
Avik Banerjee, Hridoy R Bairagya, Bishnu P Mukhopadhyay*, Tapas K Nandi, and Deepak K Mishra
Conserved water mediated H-bonding dynamics of Ser 117 and Thr 119 residues in human transthyretin - thyroxin complexation: Inhibitor modeling study through docking and molecular dynamics simulation
Journal of Molecular Graphics and Modelling, 44, 70-80, 2013.
Bornali Chakrabarti, Hridoy R Bairagya, Deepak K Mishra, Pradip Kumar Chatterjee, and Bishnu P Mukhopadhyay*
Insight towards the conserved water mediated recognition of catalytic and structural Zn+2 ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods. Bioinformation, 126-133, 9(3), 2013.
Deepak K,Mishra, Bishnu P.Mukhopadhyay*, and Hridoy R.Bairagya
Molecular Modeling of Inosine 5’-Monophosphate Dehydrogenase-II (Human) Structure using MD simulation methods. International Journal of Pharma and Bio Sciences 3(4): (B) 102 – 120, 2012.
Tapas K Nandi, Hridoy R Bairagya, Deepak K Mishra, Bishnu P Mukhopadhyay*,and Avik Banerjee
Structural and Putative Functional Role of Conserved Water Molecular Cluster in the X- ray structures of Plant Thiol Proteases:A Molecular Dynamics Simulation Study. Journal of Chemical Crystallography 42(11), 1105-1118, 2012.
Tapas K Nandi, Hridoy R Bairagya, Bishnu P Mukhopadhyay*, Payel Mallik, Dipankar Sukul, and Asim K Bera
Conserved water mediated H-bonding dynamics of catalytic His 159 and Asp158 : An insight to possible acid – base coupled mechanism in plant thiol protease. Journal Molecular Modeling 18(6), 2633-2644, 2012.
B.Ghosh, Bishnu .P. Mukhopadhyay*, and Hridoy R. Bairagya
Effect of amino acids on bioleaching of chalcopyrite ore by Thiobacillus ferrooxidans.
African Journal of Biotechnology 11(8), 1991-1996, 2012.
Bornali Chakrabarti , Hridoy R Bairagya*, Payel Mallik, Bishnu P Mukhopadhyay, and Asim K Bera
An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2 ions in Matrix Metalloproteinase 13 of Human. J. Biomolecular Structure & Dynamics 503 – 516 , 28 ( 4), 2011.
Avik Banerjee, Hridoy R Bairagya, Bishnu P Mukhopadhyay*,and Tapas K Nandi
Role of Conserved Water molecules in binding of Thyroxin and analogs inhibitors to human Transthyretin: A study on water-mimic inhibitor design. J. Biomolecular Structure & Dynamics, 28, 1027-1028, 2011.
Bishnu P Mukhopadhyay* and Hridoy R Bairagya
Protein Folding: Grand Challenge of Nature. J. Biomolecular Structure & Dynamics 337 – 338, 28 (4), 2011.
Avik Banerjee, Hridoy R Bairagya, Bishnu P Mukhopadhyay*, Tapas K Nandi, and Asim K Bera
Structural insight to mutated Y6S transthyretin by molecular dynamics simulation
Indian Journal of Biochemistry & Biophysics 47 (4)197 – 202, 2010.
Tapas K Nandi, Hridoy R Bairagya, Bishnu P Mukhopadhyay*, D . Sukul, A.K.Bera, and K. Sekar
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease.
J. Biosciences, (34) 27–34, 2009.
B.P.Mukhopadhyay*, B.Ghosh, H.R.Bairagya, T.K.Nandi, B.Chakrabarti, and A.K.Bera
Molecular Modeling of the Ternary Complex of Rusticyanin -Cytochrome c4 –Cytochrome oxidase : An Insight to Possible H- Bond Mediated Recognition & Electron Transfer Reaction in T. ferrooxidans
J. Biomolecular Structure & Dynamics, 25,5, 543- 552, 2008.
B.P.Mukhopadhyay*, B.Ghosh, H.R.Bairagya, A.K.Bera , T.K.Nandi, and S.B. Das
Modeling Study of Rusticyanin-Cytochrome C4 Complex: An Insight to Possible H-Bond Mediated Recognition and Electron Transfer Process? J. Biomolecular Structure & Dynamics , 25, 2, 157- 164, 2007.
B.P.Mukhopadhyay*, B.Ghosh, H.R.Bairagya, A.K.Bera, and R.K.Roy
Conserved Water Molecular Dynamics of the Different X-ray Structures of Rusticyanin: An Unique Aquation Potentiality of the Ligand Bonded Cu++ Center. J. of Biomolecular Structure & Dynamics, 24, 4, 369- 378, 2007.
Papers presented in International Conference :
Hridoy R. Bairagya
New Biochemical Insights into the Dynamics of Conserved Water Molecules at the substrate binding site of the human GMPR Enzyme. International Conference (Online) titled Biomolecules to Biome (BMB) dated 24th to 25th August 2022 at the Department of Life Sciences, Presidency University, Kolkata.
Hridoy R. Bairagya* and Alvea Tasneem
Impact of Conserved Water Molecules in hGMPR Enzyme. PDB 50th Anniversary Symposium in Asia (online symposium) dated on 24th November.2021. e-Poster Presentation and format of poster: Movie.
Hridoy R. Bairagya* and Tej. P. Singh
New structural insight of GMP binding domain in unliganded conformation of hGMPR enzyme: A MD simulation study. Multiscale Simulation & Mathematical Modelling of Complex Biological Systems from 30-01-2019 to 1-02-2019 at Jawaharlal Nehru University, New Delhi, India.
Deepak K. Mishra, Hridoy R. Bairagya, and Bishnu P. Mukhopadhyay
Role of conserved water molecular triad in the recognition of IMP,NAD+ with Asp 274, Asn 303, Arg322, and Asp 364 in both the isoform of hIMPDH.State University of New York, Albany 2013: The 18th Conversation, June -2013. 31 (S1),111, 2013.
Hridoy R Bairagya, Bishnu P Mukhopadhyay, and Sunav Dutta.
The Invariant Aquation Potentiality of the Active site Residues of Human IMPDH II. International Conference on Bioinformatics. December 20th -22th, 2007 at University of Hyderabad.
6.B.Ghosh, B.P.Mukhopadhyay, and H.R.Bairagya
Invariant water molecular interaction in the acidophilic redox protein Rysticyanin of Thiobacillus ferroxidans. International Symposium on Computational Biology & Bioinformatics (ISBB 06) 15th -17th December 2006 at Bhubanswar.
7. B.Ghosh, B.P.Mukhopadhyay, and H.R.Bairagya
Modeling studies of the Rysticyanin –Cytochrome C4 Complex Involving in the Thiobacillus ferroxidans During the Electron Transfer Reaction. International Symposium on Computational Biology &Bioinformatics. (ISBB 06) 15th -17th December 2006 at Bhubanswar.
8. Bishnu P Mukhopadhyay and Hridoy R Bairagya
Molecular Dynamics Study of IMPDH II ( Inosine Monophosphate Dehydrogenase) and its Complexes : A Probe to Design Potent Anticancer Agents / Inhibitors. International Symposium on Recent Trends in Macromolecular Structure and Function (“ISRTMSF 2008”) at Madras University, 7th – 11th January, 2008.
9. Bishnu P Mukhopadhyay, Hridoy R Bairagya, and B. Chakrabarti
Molecular Dynamics Study of Matrix Metalloproteinase (MMP - 13) : An Insight to Hydration Propensity at Active Zn+2 site.
International Symposium on Recent Trends in Macromolecular Structure and Function (“ISRTMSF 2008”) at Madras University, 7th – 11th January, 2008.
Publications (National Conference):
List of Papers presented in National Conference: (34)
1.Debapriyo. Sarmadhikari, Hridoy R. Bairagya*
Impact of Conserved Water Molecules in the Catalytic Domain of Mpro Protein: A Study by Molecular Dynamic Simulation. National Conference on Molecular Modelling and Simulations (NCMMS-2022). School of Advanced Sciences and Languages (SASL), VIT Bhopal University. February 28 – March 02, 2022.
2. Saborno Boral, Hridoy R. Bairagya*
Investigation the Inhibitors of hGRK2 Protein : A Computational Drug Discovery Study for Cardiovascular Disease. National Conference on Molecular Modelling and Simulations (NCMMS-2022). School of Advanced Sciences and Languages (SASL), VIT Bhopal University. February 28 – March 02, 2022.
3. Archita Bhattacherjee, Hridoy R. Bairagya*
Structural and Dynamical role of conserved water molecules in Glutamine amio transferase domain of hGMPs enzyme : A study by molecular dynamics simulations. National Conference on Molecular Modelling and Simulations (NCMMS-2022). School of Advanced Sciences and Languages (SASL), VIT Bhopal University. February 28 – March 02, 2022.
4. Hridoy R. Bairagya*
New Biochemical Insights into the Dynamics of Water Molecules at the substrate binding Site of human GMPR Enzyme. 44th Indian Biophysical Society Meeting (IBS 2022). ACTREC, Tata Memorial Centre, Navi Mumbai, 30th March to 1st April, 2022.
5. Debapriyo Sarmadhikari and Hridoy R. Bairagya*
Investigation of invariant water molecules in the native conformation of Mpro protein. 44th Indian Biophysical Society Meeting (IBS 2022). ACTREC, Tata Memorial Centre, Navi Mumbai, 30th March to 1st April, 2022.
6. Sabarno Baral, Hridoy R. Bairagya*
Role of Conserved Water Molecules in GβGγ bound and unbound conformation in hGRK2 enzyme:A Data Mining Approach. 44th Indian Biophysical Society Meeting (IBS 2022). ACTREC, Tata Memorial Centre, Navi Mumbai, 30th March to 1st April, 2022.
7.Archita Bhattacharjee, Hridoy R. Bairagya *
Comparative Study of Water Molecule between hGMPs and nhGMPs Enzyme: Investigation by Structural Bioinformatics Method. 44th Indian Biophysical Society Meeting (IBS 2022). ACTREC, Tata Memorial Centre, Navi Mumbai, 30th March to 1st April, 2022.
8.Alvea Tasneem and Hridoy R. Bairagya*
Differentiation of Conserved Water Molecules at Substrate Binding Site between Normal and Leukemic hGMPRenzyme. HEALTH 2021: Virtual International Conference on “Cancer Biology: Advances and Challenges. Deshbandhu College, (Delhi University) New Delhi, November 11th to 13th , 2021.
9. Gyan Prakash Rai, Saima Reyaz , Alvea Tasneem, and Hridoy R. Bairagya*
Role of conserved water molecules at GMP binding site in human GMPR enzyme: A study by MD Simulation. International Conference on Frontiers in Biochemistry and Biotechnology: Strategies to Combat Human Diseases at Department of Biochemistry of Shivaji College and South Campus, University of Delhi from 12th to 13th February,2020.
10. Alvea Tasneem and Hridoy R. Bairagya*
Role of conserved water molecules in nucleotide binding domain of human GMPR enzyme: A MD Simulation study.National Seminar on Bioinformatics: Concepts, Applications & Skill Development at Department of Botany Multanimal Modi College Modinagar, Ghaziabad, (U.P.)-201204 dated 8th February,2020.
11. Gyan Prakash Rai, Saima Reyaz , Alvea Tasneem, and Hridoy R. Bairagya*
Role of conserved water molecules at GMP binding site in human GMPR enzyme: A study by MD Simulation. National Seminar on Bioinformatics: Concepts, Applications & Skill Development at Department of Botany Multanimal Modi College Modinagar, Ghaziabad, (U.P.)-201204 dated 8th February,2020.
12. Gyan Prakash Rai and Hridoy R. Bairagya*
New structural insight of GMP binding domain in unliganded conformation of hGMPR enzyme: A MD simulation study. National Workshop (9th) on Translational Bioinformatics at Department of Computer Science, Jamia Millia Islamia, New Delhi from 6th March to 7th March,2019.
13. Saima Reyaz and Hridoy R. Bairagya*
Structural and functional role salt bridges in catalytic domain of human GMPR enzyme: A study by MD simulation method. National Workshop (9th) on Translational Bioinformatics at Department of Computer Science, Jamia Millia Islamia, New Delhi from 6th March to 7th March,2019.
14. Alvea Tasneem and Hridoy R. Bairagya*
Role of Conserved Water Molecules in Nucleotide Binding Domain of hGMPR Enzyme: MD simulation study. National Workshop (9th) on Translational Bioinformatics at Department of Computer Science, Jamia Millia Islamia, New Delhi from 6th March to 7th March,2019.
15. Hridoy R.Bairagya* and Manju Bansal
New insight to oxyanion hole in unliganded conformation of GAT domain:Understanding the role of water molecules.
83rd Annual Meeting of Society Of Biological Chemists (India), held on December 17th to 21st, 2014 at KIIT-University.
16. Hridoy R.Bairagya and Manju Bansal
Water mediated recognition of catalytic His190 in GAT domain: New insight from molecular dynamics simulations.
Annual Conference of Indian Biophysical Society entitled ” Molecular Architechure,Dynamics and Assembly in Living Systems” 7th -10th February, 2014, at Saha Institute of Nuclear Physics- Kolkata.
17. Hridoy R.Bairagya and Bishnu P. Mukhopadhyay
Recognition of Gln36 and Thr152 in GATse domain of hGMPS enzyme: An investigation by M.D. Simulation. 42 National Seminar on Crystallography, November 21st to 23rd, 2013 at Department of Biophysics, All India Institute of Medical Sciences-New Delhi.
18. H. R. Bairagya and B. P. Mukhopadhyay
The design of isoform specific anti leukemic agent using conserved water Molecular Dynamics of human IMPDH.
40th National Seminar on Crystallography, 26th-28th November, 2011. Department of Physics, Osmania University, Hyderabad.
19. A. Banerjee, H. R. Bairagya, D. K. mishra, and B. P. Mukhopadhyay
Dynamics of Conserved Water Molecules in the Thyroxine binding region of Human transthyretin: A MD Simulation study.
40th National Seminar on Crystallography, 26th -28th November, 2011. Department of Physics, Osmania University, Hyderaba.
20. B. Chakrabarti, H. R. Bairagya and B. P. Mukhopadhyay
Conserved Water Molecular Dynamics of Catalytic and Structural Zn2+ ions in Human Matrix Metalloproteinase I.
40th National Seminar on Crystallography, 26th -28th November, 2011. Department of Physics, Osmania University, Hyderabad.
21. T. K. Nandi, H. R. Bairagya, and B. P. Mukhopadhyay
Role of conserved water chain / cluster in plant thiol proteases: A Molecular Dynamics Simulation Study.
40th National Seminar on Crystallography, 26th -28th November, 2011. Department of Physics, Osmania University, Hyderabad.
22. B.P.Mukhopadhyay and Hridoy R Bairagya
Water Molecular Dynamics of IMPDH: A Step towards the CML-specific Inhibitors Design.
IIIrd National Conference On New Frontiers In Haematology & Oncology at Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata from Sept. 11st -12th, 2010.
23. H. R. Bairagya and B. P. Mukhopadhyay
Conserved Water Mediated Inter-domain Recognition and Dynamics of Human IMPDH isoforms: An insight to antileukemic drug selectivity.
80th annual meeting of the Society of Biological Chemists (SBS) at Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow dated on Nov. 12th – 15th, 2011.
24. B. P. Mukhopadhyay and H. R. Bairagya
Conserved Water Mediated Recognition in human IMPDH: Water Mimic Drug Design in CML Cancer.
80th annual meeting of the Society of Biological Chemists (SBS) at Central Institute of Medicinal and Aromatic Plant (CIMAP), Lucknow dated on Nov. 12th – 15th, 2011.
25. B.P.Mukhopadhyay and Hridoy R Bairagya
Water Molecular Dynamics and Recognition of Inosine Monophosphate Dehydrogenase (IMPDH)- II in Human: Hope and Scope For AntiCancer Drug Design.
Symposium On Recent Trends In Biophysics and Workshop On Emerging Techniques of Biophysics at Banaras Hindu University, Varanasi from Feb. 13th -16th, 2010.
26. Hridoy R Bairagya and B.P.Mukhopadhyay
Conserved Water Mediated Inter-Domain Recognition in IMPDH- II (Human) Symposium On Recent
Trends In Biophysics and Workshop On Emerging Techniques of Biophysics at Banaras Hindu University, Varanasi from Feb. 13th -16th, 2010.
27. B.P.Mukhopadhyay and Hridoy R Bairagya
Conserved water based inhibitor designing of human IMPDH- II: The New strategy in Structural Biology.
38th National Seminar On Crystallography, NSC-38 at University of Mysore, from Feb. 11th– 13th, 2009.
28. Avik Banerjee, Hridoy R Bairagya, and B.P.Mukhopadhyay
Structural insight to mutated Y116S Transthyretin by molecular dynamics simulations.
38th National Seminar On Crystallography, (NSC-38) at University of Mysore, from Feb. 11th – 13th, 2009.
29. B. Chakrabarti , Hridoy R Bairagya, and B. P.Mukhopadhyay
Catalytic Role of the Structural Zn2+ through water molecular coordination: A New Insight to MMP 13 Collagenolytic Activity.
38th National Seminar On Crystallography, (NSC-38) at University of Mysore, from Feb. 11th–13th, 2009.
30. Hridoy R Bairagya , Sunav Dutta, and Bishnu P Mukhopadhyay
Modeling the IMPDH-II receptor in human for designing the anticancer inhibitor using MD –simulation studies.
National Symposium on Cellular and Molecular Biophysics, (NCMB-2009), dated 22nd -24th Jan., 2009 at Centre for Cellular and Molecular Biology, Hydrabad .
31. B. P. Mukhopadhyay, H. R. Bairagya, and T. K. Nandi
Molecular Modeling of the Ternary Complex of Rusticyanin -Cytochrome c4 –Cytochrome oxidase.
37th National Seminar On Crystallography , (NSC-37) at Jadavpur university, 6th – 8th February, 2008
32. Hridoy R Bairagya, B. Chakrabarti, and Bishnu P Mukhopadhyay
Invariant Water Molecular Dynamics at the Catalytic-site of IMPDH II (Inosine Monophosphate Dehydrogenase).
37th National Seminar On Crystallography, (NSC-37) at Jadavpur University, 6th – 8th February, 2008.
33. B.P.Mukhopadhyay, H.R.Bairagya, and B.Ghosh
Cu+2 leaching from Chalcopyrite ore by Thibacillus ferrooxidans in presence of amino acids.
National Seminar on Mineral Biotechnology, (NSMB 2007), 30th – 31st Jan, 2007. Regional Research Laboratory (RRL) CSIR, Bhubanswar, Orissa.
34. B.P.Mukhopadhyay, H.R.Bairagya, and B.Ghosh
Modeling study of Rusticyanin - Cytochrome C4 Complex Modeling of Human IMPDH Type I Enzyme: Computational Structure Prediction of Protein.
National Seminar on Mineral Biotechnology, (NSMB 2007), 30th – 31st Jan, 2007. Regional Research Laboratory (RRL) CSIR, Bhubanswar, Orissa.
Patents: Nil
Member of Editorial Board:
Topic Editor of the Journal Frontiers in Molecular Biosciences
i. International Journal of Molecular Biology and Biochemistry (IJMBB)
ii. Advances in Applied Mathematical Biosciences (AAMB)
iii. Bioinformatics & Proteomics Open Access Journal (BPOJ)
Reviewer of the Journal:
Nature Scientific Report
Microbial Pathogenesis
Journal of Biomolecular Structure and Dynamics
Frontiers Pharmacology
Journal of Molecular Modeling
Member of the Academic Committee:
Convener of Drug Awareness Committee of MAKAUT.
Ambassador of the Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology (Govt. of West Bengal), Haringhata, WB. to motivate the students to participate in academic and cultural activities.
Member of Ph.D. Committee at Bioinformatics Department, Maulana Abul Kalam Azad University of Technology (Govt. of West Bengal), Haringhata, WB.
University paper setters of M.Sc. Bioinformatics course at Department of Computer Science, Jamia Millia Islamia, New Delhi.
Professional Recognitions:
i. Life Member of Indian Crystallographic Association: (LM284)
ii. Life Member of Indian Biophysical Society: (LM 634)
iii. Life Member of Society of Biological Chemists: (Life Member. NO.: 2582)