Biochemistry, Immunology, Virus, Modeling

1. Urmi ROY June 2020
_____________________________________________________________
Contact Information
Department of Chemistry & Biomolecular Science
Clarkson University, Potsdam, NY 13699-5820
E-mail: urmi@clarkson.edu
Web: https://people.clarkson.edu/~urmi/
ORCID ID: https://orcid.org/0000-0003-0928-0574
ResearchGate Profile
Google Scholar Citation
Education
Ph.D., Indian Institute of Chemical Biology, Jadavpur University, Calcutta, India (2002)
Specialization: Nuclear Medicine and Drug Design
Doctoral Thesis: Kit Formulation of Technetium-99m Cysteine For Myocardial Infarct
Imaging. Thesis Adviser: Late Dr. Some Nath Banerjee, Former Assistant Director &
Head, Department of Nuclear Medicine, Indian Institute of Chemical Biology, Calcutta,
India
M.Sc., Zoology, Calcutta University, India (1992)
Specialization: Advanced Cytology & Genetics
Standing: First Class (equivalent overall letter grade: A)
B.Sc., Zoology (Honors), with minors in Chemistry and Botany, Calcutta University,
India (1990). Standing: Second Class (equivalent overall letter grade: B+)
Present Affiliation
• Adjunct Research Associate Professor, Department of Chemistry & Biomolecular
Science, Clarkson University, Potsdam, NY 13699
Research Interests
My current research interest is in the field of Structural Biology, and I am particularly
interested in Protein Chemistry and Protein Modeling. My research focuses mostly on
the molecular interactions between ligands and receptors, and I am interested in exploring
their applications for innovative drug discovery. The specific aspects of my ongoing
research are:

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• Modeling of Receptor Proteins
• Protein-Peptide/Protein-Protein Docking
• Identification of Ligand-Receptor Interactions at the Interface
• Solvation Effect (Explicit Solvation and Molecular Dynamics Simulation)
• Protein-Protein Interaction (PPI) Network: Identification of Functional Partners
for Potential Protein Receptor using PPI Network
• Structural Immunology (computational) and Immunoinformatics
• Educational Protein Modeling for Undergraduates
Recent Research Collaborations
Research experience in the areas of Biochemistry, Structural Biochemistry, Proteomics
and Protein Modeling in collaboration with research groups at Clarkson University.
Past Appointments
• Visiting Research Associate Professor, Department of Chemistry & Biomolecular
Science, Clarkson University, Potsdam, NY 13699 (2012-2013)
• Senior Research Fellow, Department of Nuclear Medicine, Indian Institute of
Chemical Biology, Calcutta, India (1995-1999)
• Junior Research Fellow, Dept of Nuclear Medicine, Indian Institute Of Chemical
Biology, Calcutta, India. (1993-1995)
Publications and Patent
23. 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 “Nature Public Health Emergency Collection”
(Public Health Emergency COVID-19 Initiative).
22. 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.
21. 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.
20. 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).

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19. 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
18. 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.
17. Book Chapter: U. Roy, A. G. Woods, I. Sokolowska, C. C. Darie, Utility of
Computational Structural Biology in Mass Spectrometry, Chapter 6. Advancements of
Mass Spectrometry in Biomedical Research 806, 107-128 (2014) Eds. A. G. Woods & C.
C. Darie, Advances in Experimental Medicine and Biology Series. ISBN 978-3-319-
06067-5, Springer.
16. A. G. Ngounou Wetie, I. Sokolowska, A. G. Woods, U. Roy, K. Deinhardt, C. C.
Darie, Protein-protein interactions: switch from classical methods to proteomics and
bioinformatics-based approaches, Cellular and Molecular Life Sciences, 71 205-228
(2014). – Review.
15. U. Roy, A. G. Woods, I. Sokolowska, C. C. Darie, Structural investigation of HSP70-
HSP90 and HSP90-TDF interactions. Mod Chem Appl 2: 126 (2014).
14. U. Roy, A. G. Woods, I. Sokolowska, C. C. Darie, Structural Evaluation and
Analyses of Tumor Differentiation Factor. The Protein Journal, 32 512-518 (2013).
13. I. Sokolowska, A. G. Ngounou Wetie, U. Roy, A. G. Woods, and C. C. Darie, Mass
spectrometry Investigation of Glycosylation on the NXS/T Sites in Recombinant
Glycoproteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834
1474–1483 (2013).
12. A. G. Ngounou Wetie, I. Sokolowska, A. G. Woods, U. Roy, J. A. Loo, C. C. Darie,
Investigation of stable and transient protein-protein interactions: past, present and future,
Proteomics, 13, 538–557 (2013) –Review. Included in the Journal's Special Issue:
“REVIEWS 2013”.
Most Accessed Article in 8/2013, 9/2013, 10/2013 and 11/2012–10/2013.
11. I. Sokolowska, A. G. Woods, M. A. Gawinowicz, U. Roy, and C. C. Darie,
Characterization of Tumor Differentiation Factor (TDF) and its receptor (TDF-R),
Cellular and Molecular Life Sciences, 70, 2835-2848 (2013) –Review.
10. U. Roy, I. Sokolowska, A. G. Woods, C. C. Darie, Tumor differentiation factor
(TDF) and its receptor (TDF-R): is TDF-R an inducible complex with multiple docking
sites?, Mod Chem Appl 1 (3) (2013). Most Viewed Article.

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9. U. Roy, I. Sokolowska, A. G. Woods, C. C. Darie, Structural investigation of Tumor
Differentiation Factor (TDF), Biotechnology and Applied Biochemistry, 59, 445-450
(2012). This article was selected for Editor's Choice: Nov/Dec 2012 - Jan/Feb 2013.
Most Accessed 1/2013–12/2013.
8. I. Sokolowska, A. G. Woods, M. A. Gawinowicz, U. Roy, and C.C. Darie,
Identification of a potential tumor differentiation factor receptor candidate in prostate
cancer cells, FEBS Journal, 279, 2579–2594 (2012).
7. I. Sokolowska, A. G. Woods, M. A. Gawinowicz, U. Roy, and C.C. Darie,
Identification of a potential tumor differentiation factor (TDF) receptor from steroid-
responsive and steroid-resistant breast cancer cells, The Journal of Biological Chemistry,
287, 1719-33 (2012).
6. U. Roy and L. A. Luck, Cysteine residues in heavy metal binding proteins: structural
insights and comparison with leucine binding protein, Journal of Chemistry and
Chemical Engineering, 5, 771-777 (2011).
5. M.C. Debnath, U. Roy, K.K. Halder, B.R. Sarkar, S. Sinha and S. Ganguly,
Technetium-99m cysteine; A novel radiopharmaceutical for detection of experimental
myocardial infarction in rats, Current Radiopharmaceuticals, 3, 290-296 (2010).
4. U. Roy and L. A. Luck, Molecular modeling of estrogen receptor using molecular
operating environment, Biochemistry and Molecular Biology Education. 35, 238-243.
(2007).
[This undergraduate educational paper was highlighted as an explicatory contemporary
paper on structural biochemistry published in BAMBED, RCSB PDB Newsletter, Summer
2008, Number 38, Education Corner].
3. U. Roy, M. Chatterjee Debnath, K. Sanyal, M. K. Das, S. Banerjee , Role of protecting
groups in the preparation of thiolate complexes of technetium -99m using cysteine as a
model, Journal of Labelled Compounds and Radiopharmaceuticals 49, 10, 835-847
(2006).
2. U. Mitra, S.Mukherjee and S. Banerjee, Sulpher to nitrogen benzoyl transfer in
protected aminothiol ligand, Indian Journal of Nuclear Medicine, Issue 1, January 1995
[Published under my maiden name].
1. S. Banerjee, U. Mitra, M. Chatterjee, A process for the preparation of technetium
chelates with thiolate protected ligands useful for nuclear imaging study, Indian patent
filed number 613/DEL/2000 [Patent filed under my maiden name].
h-index: 10 (Source: Google scholar)

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Recent Presentations and Posters
16. 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.
15. 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.
14. 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.
13. A. G. Ngounou Wetie, I. Sokolowska, U. Roy, A. G. Woods, and C. C. Darie, Mass
Spectrometry Analysis of NXS/T Glycosylation Sites in Recombinant Glycoproteins -
Poster presented at 2014 Eastern Analytical Symposium & Exposition (EAS), November
2014, Somerset NJ.
12. Guest Lecturer for Biochemistry course (BY450/BY650/CM460/CM560), “Protein
Structure”, September 2014, Clarkson University, Potsdam, NY.
11. A. G. Ngounou Wetie, I. Sokolowska, U. Roy, A. G. Woods, and C. C. Darie, Mass
Spectrometry Analysis of NXS/T Glycosylation Sites in Recombinant Glycoproteins -
Poster presented at i) 62nd
ASMS Conference on Mass Spectrometry and Allied Topics,
June 16, 2014, Baltimore Convention Center, Baltimore, MD.; ii) The 10th
Annual
Protein and Antibody Engineering Summit (PEGS), May 2014, Boston, MA.; iii)
Graduate Student Symposium, May 20, 2014, SUNY Buffalo, Buffalo, NY.; iv) NNY
ACS Meeting - Fifth Annual Undergraduate and Graduate Chemistry & Biology
Research Symposium, April 26, 2014, SUNY Plattsburgh, Plattsburgh, NY.
10. U. Roy, A. G. Woods, C. C. Darie, Molecular Dynamics Simulation of Tumor
Differentiation Factor Peptide (TDF-P1), Poster presented at CAMP Annual Technical
Meeting, May 15 2014, Saratoga Springs, NY.
9. K. L. Wormwood, A. G. Ngounou Wetie, I. Sokolowska, K. M. Beglinger, J. W.
Mattingly, U. Roy, J. P. Ryan, A. G. Woods, C. C. Darie, Proteomic Investigation of
Sera and Saliva from Children with Autism Spectrum Disorder and Matched Controls,
Poster presented at i) Graduate Student Symposium, May 20, 2014, SUNY Buffalo,
Buffalo, NY.; ii) NNY ACS Meeting - Fifth Annual Undergraduate and Graduate
Chemistry & Biology Research Symposium, April 26, 2014, SUNY Plattsburgh,
Plattsburgh, NY.

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8. A. G. Ngounou Wetie, I. Sokolowska, U. Roy, A. G. Woods, C.C. Darie, Proteomic
Investigation of the Tumor Differentiation Factor (TDF)-induced Cell Differentiation,
Poster presented at The 2nd Annual School of Arts & Science Graduate Student
Symposium, December 6th, 2013, Clarkson University, Potsdam, NY.
7. Guest Lecturer for Biochemistry course (BY450/BY650/CM460/CM560), “3D Protein
Structure”, September 2013, Clarkson University, Potsdam, NY.
6. K. L. Wormwood, A. G. Ngounou Wetie, I. Sokolowska, K. M. Beglinger, J. W.
Mattingly, U. Roy, J. P. Ryan, A. G. Woods, C. C. Darie, Proteomic Investigation of Sera
and Saliva from Children with Autism Spectrum Disorder and Matched Controls, - Poster
presented at i) 16th Annual SURE, August 1, 2013, Clarkson University, NY.; ii) The
2013 Smith-Lemli-Opitz Family and Medical Conference, June, 2013, Pittsburgh, PA.;
iii) 61ST ASMS Conference on Mass Spectrometry and Allied Topics, June 13, 2013,
Minneapolis Convention Center, Minneapolis, Minnesota.; iv) NNY ACS Meeting, April
20, 2013, Saint Lawrence University, Canton, NY.; v) 15th Annual SURE, April 13,
2013, Clarkson University, NY.
5. K. M. Beglinger, A. G. Ngounou Wetie, I. Sokolowska, K. L. Wormwood, J. W.
Mattingly, U. Roy, J. P. Ryan, A. G. Woods and C. C. Darie, Proteomic investigation of
saliva from children with Autism Spectrum Disorder (ASD) and matched controls during
circadian rhythmicity, - Poster presented at i) The 2013 Smith-Lemli-Opitz Family and
Medical Conference, June, 2013, Pittsburgh, PA.; ii) 61ST ASMS Conference on Mass
Spectrometry and Allied Topics, June 13, 2013, Minneapolis Convention Center,
Minneapolis, Minnesota.; iii) NNY ACS Meeting, April 20, 2013, Saint Lawrence
University, Canton, NY.; iv) 15th Annual SURE, April 13, 2013, Clarkson University,
NY.
4. A. G. Ngounou Wetie, I. Sokolowska, P. Yang; U. Roy, A. G. Woods, C.C. Darie,
Proteomic Investigation of the Tumor Differentiation Factor (TDF)-induced Cell
Differentiation, Poster presented at 61ST ASMS Conference on Mass Spectrometry and
Allied Topics, June 10, 2013, Minneapolis Convention Center, Minneapolis, Minnesota.
3. I. Sokolowska, A. G. Ngounou Wetie, U. Roy, C. Talbot A. G. Woods, and C. C.
Darie, Mass Spectrometry Analysis of NXS/T Glycosylation Sites in Recombinant
Glycoproteins, Poster presented at 61ST ASMS Conference on Mass Spectrometry and
Allied Topics, June 11, 2013, Minneapolis Convention Center, Minneapolis, Minnesota.
2. U. Roy, Basic Web Design, Talk presented: International Research Experiences for
Students- Advanced Materials for a Sustainable Development (IRES-AMSD) Summer
Students, May 2013, Clarkson University, Potsdam NY.
1. U. Roy, I. Sokolowska, A. G. Woods and C. C. Darie, Structural Investigation of
Tumor Differentiation Factor (TDF) and its Receptor (TDF-R), Poster presented at
CAMP Annual Technical Meeting, May 16 2013, Saratoga Springs, NY.

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Review Service
Reviewer for American Chemical Society
Computer Skill
• Operating systems: UNIX, Linux, Windows 10/9x/me/XP/7
• Languages: Java, C++ (some), HTML, PHP, JavaScript, Visual Basic
• Database Systems: MS Access, SQL (some)
• Applications Software: Microsoft Office, Corel Draw, Adobe Photo Deluxe,
Dreamweaver, Flash, Fireworks, Origin
• Biological Modeling Package: Accelrys Discovery Studio 3.5 and 3.1; Accelrys
Materials Studio 6; Biosym/Insight II; Molecular Operating Environment (MOE);
Rasmol; Rastop; Pymol; Swiss PDB Viewer (Deepview); Protein Explorer;
Chime; Jmol; UCSF Chimera.
Recent Web Designs and Web Maintenance works
• Center for Advanced Materials Processing, Clarkson University
• Department of Chemistry & Biomolecular Science, Clarkson University
• The Shipley Center for Innovation, Clarkson University
• International Research Experiences for Students: Advanced Materials for a
Sustainable Development
Demonstrated “Web-design” Workshop for “IRES-AMSD” Summer REU
Students, Clarkson University, Potsdam, NY (May 2011, May 2012 and May
2013)
• Clarkson Club
• 79th ACS Colloid and Surface Science Symposium:
• Center for Quantum Device Technology Conference
• Numerous personal websites (mostly for various faculty members at Clarkson
University)
Community Service
• Volunteer for American Cancer Society Spring Daffodil Sale: 2000-2006
• Volunteer for Potsdam Chamber of Commerce Ives Park Planting Project: 2000
• Volunteer for American Red Cross Blood Drive: 2000
• Plant Sale Volunteer for Potsdam Humane Society: 2003
• Clarkson Club Web Designer: 2000-2007
• Volunteer Work for Haiti Relief Fund Function, Potsdam, NY: 2010

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Personal
US Citizen, Married
References
Available upon request.