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Selected Past Publications

See google scholar for full list

Sarah Welbourn, Srirupa Chakraborty, Jie E. Yang,………, S. Gnanakaran, Cynthia A. Derdeyn. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequences” – PLoS Pathogens, 18(5), p.e1010488, 2022

Srirupa Chakraborty, “MEMS-Based Strategies in Pathogen Detection” Chapter 3, MEMS Applications in Biology and Healthcare, AIP Publishing, 2021, 978-0-7354-2395-4

Will Fischer, Elena Giorgi, Srirupa Chakraborty, Kien Nguyen,………, Bette Korber, S. Gnanakaran. “HIV-1 and SARS-CoV-2: Patterns in the Evolution of Two Pandemic Pathogens” – Cell Host & Microbe, 29 (7), 1093-1110, 2021

Kien Nguyen*, Srirupa Chakraborty*, Rachael Mansbach, Bette Korber, S. Gnanakaran. “Exploring the Role of Glycans in the Interaction of SARS-CoC-2 RBD and human receptor ACE2” – Viruses, 13(5), 927 2021

Srirupa Chakraborty, Kshitij Wagh, S. Gnanakaran, Cesar A. Lopez, “Parametrization of Reductive MARTINI-II Models for N-glycans: A Case Study of the HIV-1 Env Glycoprotein Dynamics” – Glycobiology, 10.1093, 2021

Rachael Mansbach*, Srirupa Chakraborty*, Kien Nguyen, David Montefiori, Bette Korber, S. Gnanakaran. “The SARS-COV-2 Spike Variant D614G Favors an Open Conformational State” – Science Advances, 7(16), p.eabf3671, 2021

Srirupa Chakraborty*, Zachary Berndsen*, Nicolas Hengartner, Bette Korber, Andrew Ward, S. Gnanakaran, “Quantification of the Resilience and Vulnerability of HIV-1 Native Glycan Shield at Atomistic Detail” – iScience 2020 DOI: 10.1016/j.isci.2020.101836.

Zachary Berndsen*, Srirupa Chakraborty*, Xiaoning Wang, Christopher Cottrell, et. al., “Visualization of the HIV-1 Env Glycan Shield Across ScalesProceedings of National Academy of Sciences USA (PNAS), 2020 202000260. DOI: 10.1073/pnas.2000260117

Rachael Mansbach, Srirupa Chakraborty, Timothy Travers, S Gnanakaran, “Graph-Directed Approach for Downselecting Toxins for Experimental Structure Determination”– Marine Drugs 18 (5) 256, 2020

Srirupa Chakraborty, Payel Das, “Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors” – Nature Scientific Reports, 2017, 7.1: 9941

Shaweta Gupta, Srirupa Chakraborty, Ridhima Vij, Anthony Auerbach, “A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip” - Long- and short-range interactions with the M2-M3 linker suggest a mechanism for acetylcholine receptor gating” – J. Gen. Physiol. 2016, 10.1085/jgp.201611673

Tapan Nayak*, Srirupa Chakraborty*, Wenjun Zheng, Anthony Auerbach, “Structural correlates of affinity in fetal versus adult endplate nicotinic receptors” – Nature Communications, 2016; 7: 11352.

Srirupa Chakraborty, W Zheng, “Decrypting structural, dynamic and energetic basis of kinesin interacting with tubulin dimer in three ATPase states by all-atom molecular dynamics simulation”, ACS Biochemistry, 2015, 54, 859–869

Prasad Purohit, Srirupa Chakraborty, Anthony Auerbach, “Function of the M1 p-helix in endplate receptor activation and desensitization” J. Physiol. 2015, 593:2851-2866

Tapan Nayak, Srirupa Chakraborty *, Iva Bruhova*, Shaweta Gupta, Wenjun Zheng, Anthony Auerbach, “Functional differences between neurotransmitter binding sites of muscle acetylcholine receptors”, Proceedings of National Academy of Sciences USA (PNAS), 2014 111(49):17660-5

Srirupa Chakraborty, "Computational modeling of structural dynamics and energetics of two allosteric proteins: Kinesins and Acetylcholine Receptors", State University of New York at Buffalo, PhD Dissertation ProQuest Publishing, 2017

* - equal contribution by authors