Published
2024: Trujillo, C., and Dutta, S. (2024) Molecular storytelling: a conceptual framework for teaching and learning with molecular case studies, Frontiers in Education, https://doi.org/10.3389/feduc.2024.1379515, Part of ISSN: 2504-284X
2024: Burley, S.K., Wu-Wu, A., Dutta, S., Ganesan, S., Zheng, S.X.F. (2024) Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019-2023. Oncogene. 43(29):2229-2243.https://doi.org/10.1038/s41388-024-03077-2
2024: Goodsell DS, Dutta S, Hudson BP, Voigt M, Burley SK, Zardecki C. (2024) Folding paper models of biostructures for outreach and education. Patterns (N Y). 5(2):100931. https://doi.org/10.1016/j.patter.2024.100931
2024: Vardar-Ulu, D., Ragab, S.E., Agrawal, S., and Dutta, S. (2024), Using augmented reality in molecular case studies to enhance biomolecular structure-function explorations in undergraduate classrooms, J Microbiol Biol Educ. 2024 Aug; 25(2): e00019-24. https://doi.org/10.1128%2Fjmbe.00019-24
2023: Bittrich, S., Bhikadiya, C., Bi, C., Chao, H., Duarte, J. M., Dutta, S., Fayazi, M., Henry, J., Khokhriakov, I., Lowe, R., Piehl, D. W., Segura, J., Vallat, B., Voigt, M., Westbrook, J. D., Burley, S. K., Rose, Y. (2023) RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances. J Mol Biol. 435(14):167994. doi: 10.1016/j.jmb.2023.167994.
2023: Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S., Ghosh, S., Goodsell, D. S., Green, R. K., Guranovic, V., Henry, J., Hudson, B. P., Khokhriakov, I., Lawson, C. L., Liang, Y., Lowe, R., Peisach, E., Persikova, I., Piehl, D. W., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Webb, B., Westbrook, J. D., Whetstone, S., Young, J.Y., Zalevsky, A., Zardecki, C. (2023), RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning, Nucleic Acids Research, Volume 51, Issue D1, D488–D508, https://doi.org/10.1093/nar/gkac1077
2022: Zardecki, C., Dutta, S., Goodsell, D. S., Lowe, R., Voigt, M., Burley, S. K. PDB-101: Educational resources supporting molecular explorations through biology and medicine. Protein Science. 2022; 31: 129– 140. https://doi.org/10.1002/pro.4200
2022: Zardecki, C., Goodsell, D. S., Dutta, S., Lowe, R., Voigt, M., Burley, S. K. (2022) PDB-101: Molecular explorations through biology and medicine. The FASEB Journal 36(S1). http://dx.doi.org/10.1096/fasebj.2022.36.S1.R4952
2022: Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P. A., Crichlow, G. V., Dalenberg, K., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J. W., Ganesan, S., Ghosh, S., Goodsell, D. S., Kramer Green, R., Guranovic, V., Henry, J., Hudson, B. P., Lawson, C. L., Liang, Y., Lowe, R., Peisach, E., Persikova, I., Piehl, D. W., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Webb, B., Westbrook, J. D., Whetstone S., Young J. Y., Zalevsky, A., and Zardecki, C. (2022) RCSB Protein Data Bank: Tools for visualizing and understanding biological macromolecules in 3D. Protein Sci. Oct 25:e4482. https://doi.org/10.1002/pro.4482
2022: Goodsell, D.S., Dutta, S., Voigt, M., Zardecki, C., Burley, S.K. (2022) Molecular explorations of cancer biology and therapeutics at PDB-101. Oncogene. 41(38):4333-4335. doi: 10.1038/s41388-022-02424-5
2022: Duarte, J.M., Dutta, S., Goodsell, D.S., Burley, S.K. (2022) Exploring protein symmetry at the RCSB Protein Data Bank. Emerg Top Life Sci.; 6(3):231-243. doi: 10.1042/ETLS20210267
2021: Burley, S.K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G.V., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., Flatt, J.W., Ganesan, S.J., Goodsell, D.S., Ghosh, S., Kramer Green, R., Guranovic, V., Henry, J., Hudson, B.P., Lawson, C.L., Liang, Y., Lowe, R., Peisach, E., Persikova, I., Piehl, D., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Vallat, B., Voigt, M., Westbrook, J., Whetstone, S., Young, J., Zardecki, C. (2021). RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein science : a publication of the Protein Society, 10.1002/pro.4213. https://doi.org/10.1002/pro.4213
2021: Zardecki, C., Dutta, S., Goodsell, D. S., Lowe, R., Voigt, M., & Burley, S. K. (2021). PDB-101: Educational resources supporting molecular explorations through biology and medicine. Protein science : a publication of the Protein Society, 10.1002/pro.4200. Advance online publication. https://doi.org/10.1002/pro.4200
2021: Riley, K.J., Vardar-Ulu, D., Pollock, E., Dutta, S. Students authoring molecular case studies as a partial course-based undergraduate research experience (CURE) for lab instruction. Biochem Mol Biol Educ. 2021; 49: 853– 855. https://doi.org/10.1002/bmb.21578
2021: Tanner, R.L., Grover, N., Anderson, M.L., Crocker, K.C., Dutta, S., Horner, A.M., Hough, L. E., Moore, T.Y., Rosen, G.L., Whitney, K.S., & Summers, A.P. (2021). Examining cultural structures and functions in biology. Integrative and comparative biology, icab140. https://doi.org/10.1093/icb/icab140
2021: Goodsell, D.S., Dutta, S., Voigt, M., Zardecki, Z. (2021) "Molecular storytelling for online structural biology outreach and education" Structural Dynamics 8, 020401; https://doi.org/10.1063/4.0000077
2021: Stebbing, J., Sánchez Nievas, G., Falcone, M., Youhanna, S., Richardson, P., Ottaviani, S., Shen, J.X., Sommerauer, C., Tiseo, G., Ghiadoni, L., Virdis, A., Monzani, F., Rizos, L.R., Forfori, F., Avendaño Céspedes, A., De Marco, S., Carrozzi, L., Lena, F., Sánchez-Jurado, P.M., Lacerenza, L.G., Cesira, N., Caldevilla Bernardo, D., Perrella, A., Niccoli, L., Méndez, L.S., Matarrese, D., Goletti, D., Tan, Y.J., Monteil, V., Dranitsaris, G., Cantini, F., Farcomeni, A., Dutta, S., Burley, S.K., Zhang, H., Pistello, M., Li, W., Romero, M.M., Andrés Pretel, F., Simón-Talero, R.S., García-Molina, R., Kutter, C., Felce, J.H., Nizami, Z.F., Miklosi, A.G., Penninger, J.M., Menichetti, F., Mirazimi, A., Abizanda, P., Lauschke, V.M. (2021) JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality. Sci Adv.;7(1):eabe4724. doi: 10.1126/sciadv.abe4724.
2021: Burley, S.K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G.V., Christie, C.H., Dalenberg, K., Di Costanzo, L., Duarte, J.M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D.S., Ghosh, S., Green, R.K., Guranović, V., Guzenko, D., Hudson, B.P., Lawson, C.L., Liang, Y., Lowe, R., Namkoong, H., Peisach, E., Persikova, I., Randle, C., Rose, A., Rose, Y., Sali, A., Segura, J., Sekharan, M., Shao, C., Tao, Y.P., Voigt, M., Westbrook, J.D., Young, J.Y., Zardecki, C., Zhuravleva, M. (2021) "RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences." Nucleic Acids Res. 2021 Jan 8;49(D1):D437-D451. doi: 10.1093/nar/gkaa1038.
2020: Burley, S.K., Bromberg, Y., Craig, P., Duffy, S., Dutta, S., Hall, B.L., Hudson, B.P., Jiang, J., Khare, S.D., Koeppe, J.R., Lubin, J.H., Mills, S.A., Pikaart, M.J., Roberts, R., Sarma, V., Singh, J., Tischfield, J.A., Xie, L., and Zardecki, C., (2020) "Virtual Boot Camp: COVID‐19 evolution and structural biolog", Biochem Mol Biol Educ. 2020;1 – 3, https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.21428
2020: Kurnat-Thoma, E., Baranova, A., Baird, P., Brodsky, E., Butte, A.J., Cheema, A.K., Cheng, F., Dutta, S., Grant, C., Giordano, J., Maitland-van der Zee, A.H., Fridsma, D.B., Jarrin, R., Kann, M.G., Keeney, J., Loscalzo, J., Madhavan, G., Maron, B.A., McBride, D.K., McKean, M., Mun, S.K., Palmer, J.C., Patel, B., Parakh, K., Pariser, A.R., Pristipino, C., Radstake, T.R.D.J., Rajasimha, H.K., Rouse, W.B., Rozman, D., Saleh, A., Schmidt, H.H.H.W., Schultz, N., Sethi, T., Silverman, E.K., Skopac, J., Svab, I., Trujillo, S., Valentine, J.E., Verma, D., West, B.J., Vasudevan, S. (2020) "Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine", Syst Med (New Rochelle), 3(1):22-35. doi: 10.1089/sysm.2020.0001. eCollection 2020. PMID: 32226924
2019: wwPDB Consortium (2019) "Protein Data Bank: The Single Global Archive for 3D Macromolecular Structure Data Jointly Managed by the Worldwide Protein Data Bank" Nucleic Acid Research
2019: Burley, S.K., Berman, H.M., Bhikadiya, C., Bi, C., Chen, L., Di Costanzo, L., Christie, C., Dalenberg K., Duarte, J., Dutta, S., Feng, Z., Ghosh, S., Goodsell, D., Green, R.K., Guranović, V., Guzenko, D., Hudson, B., Kalro, T, Liang, Y., Lowe, R., Namkoong, H., Peisach, E., Periskova, I., Prlić, A., Randle, C., Rose, A., Rose, P., Sekharan, M., Shao, C., Tan, L., Tao, W., Valasatava, Y., Voigt, M., Westbrook, J., Woo, J., Yang, H., Young, J., Zardecki, C., and Zhuravleva, M. (2019) "RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology, and energy" Nucleic Acid Research
2018: Di Costanzo, L., Dutta, S., Burley, S.K. (2018) "Amino Acid Modifications for Conformationally Constraining Naturally-Occurring and Engineered Peptide Backbones: Insights from the Protein Data Bank" Biopolymers doi: 10.1002/bip.23230
2018: Dutta, S., Eswaran, S., Sanelli, A., Bhattacharya, M., and Tempsick, R. (2018) "Learning Biology Through Molecular Storytelling" The Science Teacher, NSTA Journal
2017: Rose, P.W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A.R., Christie, C.H., Costanzo, L.D., Duarte, J.M., Dutta, S., Feng, Z., Green, R.K., Goodsell, D.S., Hudson, B., Kalro, T., Lowe, R., Peisach, E., Randle, C., Rose, A.S., Shao, C., Tao, Y.P., Valasatava, Y., Voigt, M., Westbrook, J.D., Woo, J., Yang, H., Young, J.Y., Zardecki, C., Berman, H.M., Burley, S.K. (2017) "The RCSB Protein Data Bank: Integrative View of Protein, Gene and 3D Structural Information" Nucleic Acids Res. 45(D1): D271-D281. doi: 10.1093/nar/gkw1000
2016: Zardecki, C., Dutta, S., Goodsell, D.S., Voigt, M., Burley, S. K. (2016) "RCSB Protein Data Bank: A resource for chemical, biochemical, and structural explorations of large and small biomolecules" Journal of Chemical Education 93 (3), 569-575 doi: 10.1021/acs.jchemed.5b00404
2015: Rose, P.W., Prlić, A., Bi, C., Bluhm, W.F., Christie, C.H., Dutta, S., Green, R.K., Goodsell, D.S., Westbrook, J., Woo, J., Young, J., Zardecki, C., Berman, H.M., Bourne, P., and Burley, S.K. (2015) “The RCSB Protein Data Bank: Views of Structural Biology for Basic and Applied Research and Education” Nucleic Acids Research 43(D1): D345-356 doi:10.1093/nar/gku1214
2015: Goodsell, D.S., Dutta, S., Zardecki, C., Voigt, M., Berman, H.M. and Burley, S.K. (2015) “The RCSB PDB 'Molecule of the Month': Inspiring a Molecular View of Biology” PLOS Biology doi: 10.1371/journal.pbio.1002140
2014: Dutta, S., Dimitripoulos, D., Feng, Z., Persikova, I., Sen, S., Shao, C., Westbrook, J., Young, J., Zhuravleva, M.A., Kleywegt, G., and Berman H.M. (2014) "Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank." Biopolymers 101: 659–668. doi:10.1002/bip.22434
2014: Sen, S., Young, J., Berrisford, J.M.,Chen, M., Conroy, M.J., Dutta, S., Di Costanzo, L., Gao, G., Ghosh, S., Hudson, B.P., Igarashi, R., Kengaku, Y., Liang, Y., Peisach, E., Persikova, I., Mukhopadhyay, A., Narayanan, B.C., Sahni, G., Sato, J., Sekharan, M., Shao, C., Tan, L. and Zhuravleva M.A. (2014) “Small Molecule Annotation for the Protein Data Bank” Database: bau116 doi: 10.1093/database/bau116
2013: Berman, H., Coimbatore Narayanan, B., Di Costanzo, L., Dutta, S., Ghosh, S., Hudson, B., Lawson, C.L., Peisach, E., Prlić, A., Rose, P.W., Shao, C., Yang, H., Young, J., and Zardecki, C. (2013) "Trendspotting in the Protein Data Bank" FEBS Lett. 587: 1036-45
2013: Rose, P.W., Bi, C., Bluhm, W.F., Christie, C.H., Dimitropoulos, D., Dutta, S., Green, R.K., Goodsell, D.S., Prlic´, A., Quesada, M., Quinn, G.B., Ramos, A.G., Westbrook, J.W., Young, J., Zardecki, C., Berman, H.M. and Bourne, P.E. (2013) "The RCSB Protein Data Bank: new resources for research and education" Nucleic Acids Research D475–D482, https://doi.org/10.1093/nar/gks1200
2010: Dutta, S., Zardecki, C., Goodsell, D.S., and Berman, H.M. (2010) "Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences" J. Appl. Cryst. 43:1224-1229
2008: Henrick K., Feng Z., Bluhm W.F., Dimitropoulos D., Doreleijers J.F., Dutta S., Flippen-Anderson J.L., Ionides J., Kamada C., Krissinel E., Lawson C.L., Markley J.L., Nakamura H., Newman R., Shimizu Y., Swaminathan J., Velankar S., Ory J., Ulrich E.L., Vranken W., Westbrook J., Yamashita R., Yang H., Young J., Yousufuddin M., and Berman H.M. (2008) "Remediation of the Protein Data Bank archive." Nucleic Acids Res. D426-33.
2008: Lawson C.L., Dutta S., Westbrook, J.D., Henrick, H., and Berman, H.M. (2008) "Representation of Viruses in the Remediated PDB Archive" Acta Cryst. D64, 874-882
2005: Dutta, S., and Berman. H.M. (2005) "Large macromolecular complexes in the Protein Data Bank: a status report." Structure 13, 381-388.
2004: Li, Y., Dutta, S., Doublie, S., Bdour, H.M., Taylor, J.S., and Ellenberger, T. (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat Struct Mol Biol. 8, 784-790.
2004: Yang, H., Guranovic, V., Dutta, S., Feng, Z., Berman, H.M., and Westbrook, J.D. (2004) "Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank." Acta Crystallogr D Biol Crystallogr. 60 1833-1839.
2004: Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., and Ellenberger, T. (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc Natl Acad Sci USA. 101, 16186-16191.
2003: Namboodiri, V. M. H., Dutta, S., Akey, I. V., Head, J. F., and Akey, C. W. (2003) "The Crystal Structure of Drosophila Nlp-Core Provides Insight Into Pentamer Formation and Histone Binding." Structure 11, 175-186.
2001: Dutta, S., Akey, I.V., Dingwall, C., Hartman, K.L., Laue, T., Nolte, R.T., Head, J.F., and Akey, C.W. (2001) "The Crystal Structure of Nucleoplasmin-Core: Implications for Histone Binding and nucleosome assembly." Molecular Cell, 8, 841-853.
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