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Protein Modeling and Protein
Chemistry
Protein Dynamics and Protein Simulations
Department of Chemistry & Biochemistry
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
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+)
- Adjunct Research
Associate Professor, Department of Chemistry & BioChemistry,
Clarkson University, Potsdam, NY 13699
· Courses taught at Clarkson University
Biochemistry II (BY 451, CM 461 / BY 651, CM 561; 3 Credit Hours)
Spring 2026
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:
- Predictive Protein
Modeling
- 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
- Educational Protein
Modeling for Undergraduates
- Metalloproteins and Implications
of Metal ions in Biological Systems
- Structural Immunology
(computational) and Immunoinformatics
o Immunomodulatory
and Proinflammatory Cytokines:
Implications
for Cellular Signaling Processes
o Virus
Structure
o
Host-Virus Interactions
o
Structural Biology of SARS-CoV-2: original strain, variants
and subvariants
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Recent Research Collaborations
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Research experience in the areas of Biochemistry, Structural
Biochemistry, Proteomics and Protein Modeling in collaboration with
research groups at Clarkson University.
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)
31. U. Roy, Structural Evaluation of Interleukin-19 Cytokine and
Interleukin-19-Bound Receptor Complex Using Computational
Immuno-Engineering Approach, Targets 2(4), 385-395 (2024). https://doi.org/10.3390/targets2040022.
30. 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.
29. 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.
28. 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).
27. 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.
26. 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
25. U. Roy, Role of N501Y Mutation in SARS-CoV-2 Spike Protein
Structure, (2021). Preprint doi: 10.20944/preprints202106.0238.v1
24. 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.
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 "PubMed Central
COVID-19 Collection" by Springer Nature.
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).
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,
Eds. A. G. Woods & C. C. Darie, Advances in Experimental Medicine and
Biology Series 806, 107-128
(2014). 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". PDF
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). PDF
Most Viewed Article.
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). DOI: 10.2174/1874471011003040290.
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). PDF
[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. 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). DOI: 10.2174/1874471011003040290.
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: 13
(Source: Google scholar)
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Recent Presentations and Posters
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18. 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).
17. 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.
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 NNY ACS
Meeting-- Fifth Annual Undergraduate and Graduate Chemistry & Biology
Research Symposium, April 26, 2014, SUNY Plattsburgh, Plattsburgh, NY
AND Graduate Student Symposium, May 20, 2014, SUNY Buffalo, Buffalo,
NY.
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, 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.
1. 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.
Reviewer of manuscripts for: Antioxidants, Biotechnology Journal,
Biochemistry Research International, Computers in Biology and Medicine, Computational
and Structural Biotechnology Journal, Frontiers in Oncology, International
Journal of Molecular Sciences, Journal of Cell Communication and Signaling,
Journal of Chemical Education, Journal of Physical Chemistry, Molecular
Diversity, Molecules, Nature Communications, Pharmaceuticals,
Pharmaceutics, Scientific Reports, Toxics, Viruses, Virus Genes and Virus
Research.
Operating systems: UNIX, Linux, Windows 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 4, 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.
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Recent Web Designs and Web Maintenance works
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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 Web Site
79th ACS Colloid and Surface Science Symposium
Center for Quantum Device Technology Conference
Numerous personal websites (mostly for various faculty members at
Clarkson University)
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
Available upon request.
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