Structure based Computational Immunology
and Immunoinformatics

   

Recent Publications

U. Roy, Computational Investigation of Selected Spike Protein Mutations in SARS-CoV-2: Delta, Omicron, and Some Circulating Subvariants, Pathogens 13(1), 10 (2024). https://doi.org/10.3390/pathogens13010010. This article has been included in the Special Issue "SARS-CoV-2 Variants Research and Vaccines".

P. R. Fatouros, U. Roy, S. Sur, Implications of SARS-CoV-2 Spike Protein Interactions with Zn-bound form of ACE2: A Computational Structural Study, BioMetals 36, 903-912 (2023). doi: https://doi.org/10.1007/s10534-023-00491-z. This article has been included in "PubMed Central COVID-19 Collection" by Springer Nature.

U. Roy,, Host–Virus Interactions in Japanese Encephalitis Virus, Zoonotic Disease 2(3), 117-125 (2022), https://doi.org/10.3390/zoonoticdis2030012. This article belongs to the Special Issue Feature Papers of Zoonotic Diseases 2021–2022.

U. Roy, Comparative Structural Analyses of Selected Spike Protein-RBD Mutations in SARS-CoV-2 Lineages, .Immunologic Research 70, 143-151 (2022). doi: 10.1007/s12026-021-09250-z. This article has been included in "PubMed Central COVID-19 Collection" by Springer Nature.

P. R. Fatouros, U. Roy, S. Sur, Modeling Substrate Coordination to Zn-Bound Angiotensin Converting Enzyme 2, International Journal of Peptide Research and Therapeutics 28: 2 (2022). https://link.springer.com/article/10.1007/s10989-022-10373-6

U. Roy, Role of N501Y Mutation in SARS-CoV-2 Spike Protein Structure, (2021). Preprint doi: 10.20944/preprints202106.0238.v1

U. Roy, Insight into the Structures of Interleukin-18 Systems, Computational Biology and Chemistry 88, 107353 (2020). https://doi.org/10.1016/j.compbiolchem.2020.107353. This article has been included in "PubMed Central COVID-19 Collection" by Elsevier.

U. Roy, Structural and Molecular Analyses of Functional Epitopes and Escape Mutants in Japanese Encephalitis Virus Envelope Protein Domain III, Immunologic Research 68, 81-89 (2020). https://doi.org/10.1007/s12026-020-09130-y. This article has been included in "PubMed Central COVID-19 Collection" by Springer Nature.

U. Roy, 3D Modeling of Tumor Necrosis Factor Receptor and Tumor Necrosis Factor-Bound Receptor Systems, Molecular Informatics 38 (5), 1800011 (2019). DOI: 10.1002/minf.201800011.

U. Roy, Structure and Function of an Inflammatory Cytokine, Interleukin-2, Analyzed using the Bioinformatic Approach, The Protein Journal 38, 525-536 (2019). DOI: 10.1007/s10930-019-09833-8.

U. Roy, Structural Modeling of Tumor Necrosis Factor: A Protein of Immunological Importance, Biotechnology and Applied Biochemistry 64, 454-463 (2017). DOI: 10.1002/bab.1523.
-This article has been selected as editor's choice and has also been mentioned on the journal's cover page. The inaugural “In This Issue: Issue Highlights” feature of this journal has mentioned this paper (p 453).

U. Roy, Structural Characterizations of the Fas Receptor and the Fas-Associated Protein with Death Domain Interactions, The Protein Journal 35, 51-60 (2016). doi:10.1007/s10930-015-9646-6.

U. Roy, Structural Biology of Tumor Necrosis Factor Demonstrated for Undergraduate Instruction by Computer Simulation, Biochemistry and Molecular Biology Education 44, 246-255 (2016) DOI 10.1002/bmb.20937.
-Featured article in BAMBED May/June 2016.

 

Recent Presentations

P. Fatouros*, U. Roy, S. Sur, Modeling the SARS-CoV-2 Receptor ACE2 Indicates that Protein-Bound Zn Affects Distant Protein Stability and Interactions, The Journal of Immunology (The American Association of Immunologists) 210, Issue 1_Supplement (2023) https://doi.org/10.4049/jimmunol.210.Supp.249.23.
    Presented by P. Fatouros* at IMMUNOLOGY2023 conference, Washington DC. (*Honors student co-advised with Dr. S. Sur).

P. Fatouros, S. Sur, U. Roy, Modeling Inhibitor Coordination to Zn-Bound Angiotensin Converting Enzyme 2, Talk presented by P. Fatouros* at eRAPS, Summer 2020, Clarkson University, NY.

U. Roy, Structure and Function of an Inflammatory Cytokine, Interleukin-2 and its Implications in Drug Design, Poster presented at 32nd Center for Advanced Materials Processing Annual Technical Meeting, May 21 2019, Syracuse, NY.

U. Roy, Modeling and Structure based Immunoinformatic Analysis of the Fas Receptor and the Fas-Associated Protein with Death Domain, Poster presented at 29th Center for Advanced Materials Processing Annual Technical Meeting, May 19 2016, Canandaigua, NY.

U. Roy, Insight into the Structure of Tumor Necrosis Factor: A Protein of Immunological Importance, Poster presented at 28th Center for Advanced Materials Processing Annual Technical Meeting, May 21 2015, Canandaigua, NY.

   

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A. Key interactions at the protein-protein interface.
B. RMSD profile of Fas-FADD complex as functions of time.