PUBLICATIONS (in Chronological Order)

  1. Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs.
    Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee*
    BMC Bioinformatics (2011), 12 : 195.        (pdf)
    ISSN: 1471-2105
    Publishers: BMC (Part of Springer Nature)
    2. Cited by ⇒

  2. Self Complementarity within proteins: bridging the gap between binding and folding.
    Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee*
    Biophysical Journal (2012), 102 (11): 2605-2614.        (pdf)
    ISSN: 0006-3495
    Publishers: Cell Press
    3. Cited by ⇒

  3. SARAMA: A Standalone Suite of Programs for the Complementarity Plot – A Graphical Structure Validation Tool for Proteins.
    Sankar Basu*, Dhananjay Bhattacharyya and Rahul Banerjee*
    Journal of Bioinformatics and Intelligent Control (2013), 2 (4): 321-323.        (pdf)
    ISSN: 2326-7496
    Publishers: American Scientific Publishers
    4. Cited by ⇒

  4. polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications.
    Sankar Basu and Dhananjay Bhattacharyya*
    Journal of Bioinformatics and Intelligent Control (2013), 2 (4): 316-320.        (pdf)
    ISSN: 2326-7496
    Publishers: American Scientific Publishers
    5. Cited by ⇒

  5. Applications of Complementarity Plot in error detection and structure validation of proteins.
    Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee*
    Indian Journal of Biochemistry and Biophysics, (2014), 51 (June): 188-200.        (pdf)
    ISSN: 0975-0959
    Publishers: NISCAIR
    6. Cited by ⇒

  6. Equilibrium unfolding of cyclophilin from Leishmania donovani: Characterization of intermediate states
    Sourav Roy, Sankar Basu, Alok K. Datta, Dhananjay Bhattacharyya, Dipak Dasgupta*, and Rahul Banerjee*
    International Journal of Biological Macromolecules, (2014), 69: 353-360.        (pdf)
    ISSN: 0141-8130
    Publishers: Elsevier
    7. Cited by ⇒

  7. Analysis of Stacking Overlap in Nucleic Acid Structures: Algorithm and Application
    Pavan Kumar Pingali, Sukanya Halder, Debasish Mukharjee, Sankar Basu, Rahul Banerjee,
    Devapriya Choudhuri and Dhananjay Bhattacharyya*
    Journal of Computer-Aided Molecular design, (2014), 28: 851–867         (pdf)
    ISSN: 1573-4951
    Publishers: Springer Nature
    8. Cited by ⇒

  8. SARAMAint: The Complementarity Plot for Protein-Protein Interface
    Sankar Basu, Dhananjay Bhattacharyya, and Bjorn Wallner*
    Journal of Bioinformatics and Intelligent Control, (2014), 3: 309-314.        (pdf)
    ISSN: 2326-7496
    Publishers: American Scienctific Publishers
    9. Cited by ⇒

  9. The unfolding MD-simulations of Cyclophilin: Analysed by Surface Contact Networks and their associated matrices
    Sourav Roy, Sankar Basu, Dipak Dasgupta, Dhananjay Bhattacharyya*, and Rahul Banerjee*
    PLOS ONE, (2015), 10 (11): e0142173.        (pdf)
    ISSN: 1932-6203
    Publishers: PLOS
    10. Cited by ⇒

  10. Finding correct protein-protein docking models using ProQDock.
    Sankar Basu, Bjorn Wallner*
    Bioinformatics. (2016), 32 (12): i262-i270.        (pdf)
    ISSN: 1460-2059
    Publishers: Oxford Press
    11. Presented in ISMB-2016, Orlando, Florida, USA   ↱
    Cited by ⇒

  11. DockQ: A quality measure for protein-protein docking models.
    Sankar Basu, Bjorn Wallner*
    PLOS ONE, (2016), 11 (8): e0161879         (pdf)
    ISSN: 1932-6203
    Publishers: PLOS
    12. Serves as in the quality assesment for docked protein complexes in the Protein Olympics (CAPRI)   ↱
     Cited by ⇒

  12. RNAHelix: Computational Modeling of Nucleic Acid Structures with Watson-Crick and Non-canonical Base pairs
    Dhananjay Bhattacharyya*, Sukanya Halder, Sankar Basu, Prasun Kumar, Debasish Mukherjee, Manju Bansal*
    Journal of Computer-Aided Molecular Design, (2017), 31 (2): 219-235        (pdf)
    ISSN: 1573-4951
    Publishers: Springer Nature
    13. Cited by ⇒

  13. Proteus: A Random Forest Classifier that Predicts Disorder-to-Order Transitioning Binding Regions in Intrinsically Disordered Proteins
    Sankar Basu, Fredrik Söderqvist, Björn Wallner*
    Journal of Computer-Aided Molecular Design, (2017), 31 (5): 453–466        (pdf)
    ISSN: 1573-4951
    Publishers: Springer Nature
    14. Cited by ⇒

  14. Salt-bridge Networks within Globular and Disordered Proteins - Characterizing Trends for Designable Interactions.
    Sankar Basu* and Debasish Mukharjee
    Journal of Molecular Modeling, (2017), 23: 206        (pdf)
    ISSN: 0948-5023
    Publishers: Springer Nature
    15. Cited by ⇒

  15. Nitric oxide sensing by chlorophyll-a
    Abhishek Bhattacharya, Pranjal Biswas, Puranjoy Kar, Piya Roychoudhury, Sankar Basu, Souradipta Ganguly, Sanjay Ghosh, Kaustab Panda, Ruma Pal, Anjan Kr. Dasgupta*
    Analytica Chemica Acta, (2017), 985: 101-113        (pdf)
    ISSN: 0003-2670
    Publishers: Elsevier
    16. Cited by ⇒

  16. CPdock: The Complementarity Plot for Docking of Proteins: Implementing Multi-dielectric Continuum Electrostatics
    Sankar Basu*
    Journal of Molecular Modeling, (2018), 24: 8         (pdf)
    ISSN: 0948-5023
    Publishers: Springer Nature
    17. Cited by ⇒

  17. Salt-bridge Dynamics in Intrinsically Disordered Proteins: A trade-off between electrostatic interactions and structural flexibility
    Sankar Basu and Parbati Biswas*
    BBA Proteins and Proteomics, (2018), 1866 (5-6): 624-641         (pdf)
    ISSN: 1570-9639
    Publishers: Elsevier
    18. Cited by ⇒

  18. Inner-view of nanomaterial incited protein conformational changes: Insights in designable interaction.
    Arka Mukhopadhyay$, Sankar Basu$, Santiswarup Singha and Hirak K Patra*    
    Research (Science partner Journal), (2018), 1: 9712832         ($: Equal Authorship)    (pdf)      (Review Paper)
     ISSN: 2639-5274
    Publishers: American Association for the Advancement of Science (AAAS)
    19. Art-work from the paper appeared as front cover in the inaugural Journal issue.
    Cited by ⇒

  19. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate
    Swagata Pahari, Lexuan Sun, Sankar Basu, Emil Alexov*
    Proteins: Structure, Function and Bioinformatics, (2018), 86 (12): 1277-1283         (pdf)
    ISSN: 1097-0134
    Publishers: Wiley
    20. Cited by ⇒

  20. Structural perspective on revealing and altering molecular mechanisms of genetic variants linked with diseases.
    Yunhui Peng, Emil Alexov, Sankar Basu*
    International Journal of Molecular Sciences, (2019), 20 (3): 548         (pdf)      (Review Paper)
     ISSN: 1422-0067
    Publishers: MDPI
    21. Cited by ⇒

  21. DelPhi suite: New developments and review of functionalities
    Chuan Li*, Zhe Jia, Arghya Chakravorty, Swagata Pahari, Yunhui Peng, Sankar Basu, Mahesh Koirala, Shailesh Kumar Pandey, Marharyta Petukh, Lin Li, Emil Alexov*
    Journal of Computational Chemistry, (2019), 40 (28): 2502-2508        (pdf)
    ISSN: 1096-987X
    Publishers: Wiley
    22. Cited by ⇒

  22. Graph Coloring: A Novel Heuristic Based on Trailing Path, Perspective and Applications in Structured Networks.
    Abhirup Bandyopadhyay, Amit Kumar Dhar, Sankar Basu*
    Soft Computing (2019), 24: 603-625        (pdf)
    ISSN: 1432-7643
    Publishers: Springer Nature
    23. Media Coverage:   ↱
    Cited by ⇒

  23. A comprehensive computational study of amino acid interactions in membrane proteins
    Mame Ndew MbayeY, Qingzhen HouY, Sankar Basu, Fabian Teheux, Fabrizio Pucci, Marianne Rooman*
    Scientific Reports (2019), 9: 12043        (pdf)
    ISSN: 2045-2322
    Publishers: Nature Portfolio
    24. Cited by ⇒

  24. Criticality in the conformational phase transition among self-similar groups in intrinsically disordered proteins: probed by salt-bridge dynamics
    Abhirup Bandyopadhyay, Sankar Basu*
    BBA Proteins and Proteomics (2020), 1868 (10): 140474         (pdf)
    ISSN: 1570-9639
    Publishers: Elsevier
    25. Cited by ⇒

  25. Plausible Blockers of Spike RBD in SARS-CoV2 – Molecular Design and Underlying Interaction Dynamics from High-Level Structural Descriptors
    Sankar Basu*, Devlina Chakravarty, Dhananjay Bhattacharyya, Pampa Saha, Hirak Kumar Patra
    Journal of Molecular Modeling (2021), 27 (6): 191         (pdf)
    ISSN: 0948-5023
    Publishers: Springer Nature
    26. Cited by ⇒

  26. Review 2: "Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster"
    Sankar Basu
    Rapid Reviews COVID-19, (2021), DOI: 10.1162/2e3983f5.9b9fd405          (Invited Preprint Review)     (pdf)
    ISSN: 2692-4072
    Publishers: MIT Press & UC Berkeley
    Cited by ⇒

  27. Editorial for the Special Issue on ‘Coronavirus: Vaccines and Other Therapeutics’ (2020-21)
    Sankar Basu*
    Vaccines (2021), 9 (10): 1083        (pdf)
    ISSN: 2076-393X
    Publishers: MDPI
    Cited by ⇒

  28. BRANEart: identify stability strength and weakness regions in membrane proteins
    Sankar Basu, Simon S. Assaf, Fabian Teheux, Marianne Rooman*, Fabrizio Pucci*
    Frontiers in Bioinformatics (2021), 1: 742843.         (pdf)
    ISSN: 2673-7647
    Publishers: Frontiers
    Cited by ⇒

  29. Capturing a crucial 'disorder-to-order transition' at the heart of the coronavirus molecular pathology – triggered by highly persistent, interchangeable salt-bridges
    Sourav Roy, Prithwi Ghosh, Abhirup Bandyapadhyay, Sankar Basu*
    Vaccines (2022), 10: 301.         (pdf)
    ISSN: 1422-0067
    Publishers: MDPI
    Cited by ⇒

  30. Can the Jigsaw Puzzle Model of Protein Folding Re-assemble a Hydrophobic Core?
    Gargi Biswas, Semanti Ghosh*, Sankar Basu, Dhananjay Bhattacharyya, Alok Kumar Datta, Rahul Banerjee*
    Proteins: Structure, Function and Bioinformatics (2022), 1-23         (pdf)
    ISSN: 1097-0134
    Publishers: Wiley
    Cited by ⇒

  31. Editorial: From the Hydrophobic Core to the Globular-Disorder Interface: New Challenges and Insights into Protein Design
    Sankar Basu*, Devlina Chakravarty, Qingzhen Hou, Vladimir N. Uversky*
    Frontiers in Molecular Biosciences (section: Structural Biology) (2023), vol:10; DOI:10.3389/fmolb.2023.1151676         (pdf)
    ISSN: 2296-889X
    Publishers: Frontiers
    Cited by ⇒

  32. On the Origin Debate and Plausible Future Endeavors of COVID-19.
    Debdatta Nandy, Bijit Chatterjee, Sankar Basu*
    In S. Bhattacharya, S. Mukhopadhyay & A. Kundu (Eds.). Virus: Impacts (2023) pp. 25-41. Kolkata.            (Book chapter, Commentary)
    (preprint at Preprints, doi: 10.20944/preprints202310.1717.v1)
    ISBN: 978-81-956797-5-1
    Publishers: Research Committee and Publication Cell, Asutosh College, Kolkata, India.

  33. Phosphorylcholine and KR12-containing Corneal Implants in HSV-1 infected Rabbit Corneas
    Kamal Malhotra, Oleksiy Buznyk, Mohammad Mirazul Islam, Elle Edin, Sankar Basu, Marc Groleau, Delali Shana Dégué, Per Fagerholm, Adrien Fois, Sylvie Lesage, Jaganmohan R. Jangamreddy, Egidijus Šimoliūnas, Aneta Liszka, Hirak K. Patra*, May Griffith*
    Pharmaceutics. (2023), 15(6):1658; DOI: https://doi.org/10.3390/pharmaceutics15061658         (pdf)
    ISSN: 1999-4923 (Online)
    Publishers: MDPI
    Cited by ⇒

  34. EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations
    Gargi Biswas, Debasish Mukherjee, Nalok Dutta, Prithwi Ghosh, Sankar Basu*
    Journal of Molecular Modeling (2023) 29:239 DOI: https://doi.org/10.1007/s00894-023-05626-0         (pdf)
    ISSN: 0948-5023
    Publishers: Springer Nature
    Cited by ⇒

  35. Combining Complementarity and Binding Energetics in the assessment of Protein Interactions: EnCPdock—A Practical Manual
    Gargi Biswas, Debasish Mukherjee, Sankar Basu*
    Journal of Computational Biology (2024) 31:8 DOI: https://doi.org/10.1089/cmb.2024.0554         (pdf)
    ISSN: 1557-8666 (Online)
    Publishers: Mary Ann Liebert

  36. Plot-Tools in Protein Structure Validations: From the Ramachandran Plot to the Complementarity Plot
    Sankar Basu*
    Preprints, (2023) DOI: https://www.preprints.org/manuscript/202311.0741/v1
    (Chapter in ‘Critical studies in Science’, Research & Development cell, Asutosh College)        (Book Chapter, Commentary)
    Publishers: Asutosh College Publication cell


  37. Modified Host Defence Peptide GF19 slows TNT-mediated spread of Corneal Herpes Simplex Virus Serotype I Infection
    Neethi C Thathapudi, Natalia Callai Da Silva, Kamal Malhotra, Sankar Basu, Mozhgan Aghajanzadeh-Kiyaseh, Mostafa Zamani-Roudbaraki, Marc Groleau, Felix Lombard, Sylvie Lesage, May Griffith,*
    Scientific Reports (2024) 14:4096 DOI: https://doi.org/10.1038/s41598-024-53662-4        (pdf)
    ISSN: 2045-2322 (online)
    Publishers: Nature Portfolio

  38. Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multi-functionality
    Asifa Aftab, Souradeep Sil, Anirneya Basu, Seema Nath, Sankar Basu*
    Journal of Molecular Evolution (2024) DOI: https://doi.org/10.1007/s00239-024-10196-7   2024        (pdf)
    ISSN: 1432-1432
    Publishers: Springer


  39. Landscape of Intrinsically Disordered Proteins in Mental Disorder Diseases
    Xinwu Zhang, Yaqing Yang, Guangchun Hu, Ruotong Liu, Na Zhou, Xixi Song, Sankar Basu*, Ming Jing*, Qingzhen Hou*
    Computational and Structural Biotechnology Journal, Accepted (In-press), 2024;
    DOI:https://doi.org/10.1016/j.csbj.2024.10.043        (pdf)
    ISSN: 2001-0370
    Publishers: Elsevier

    		40.