Publications

Tatiana Shugaeva, Rebecca J. Howard, Nandan Haloi, Erik Lindahl
October, 2025 In Communications Chemistry
Modeling cryo-EM structures in alternative states with phaFold2-based models and density-guided simulations
Modeling cryo-EM structures in alternative states with phaFold2-based models and density-guided simulations
DOI
Nandan Haloi, Rebecca J. Howard, Erik Lindahl
July, 2025 In PLOS Computational Biology
Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics
Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics
DOI
Samuel Eriksson Lidbrink, Rebecca Howard, Nandan Haloi, Erik Lindahl
June, 2025 In PLOS Computational Biology
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold
Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold
DOI
Nandan Haloi, Samuel E. Lidbrink, Rebecca J. Howard, Erik Lindahl
June, 2025 In Science Advances
Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface
Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface
DOI
Nandan Haloi, Emelia Karlsson, Marc Delarue, Rebecca J. Howard, Erik Lindahl
April, 2025 In Science Advances
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3A receptor
DOI
Xiaodi Yu, Rosalie E Matico, Robyn Miller, Dhruv Chauhan, Bertrand Van Schoubroeck, Karolien Grauwen, Javier Suarez, Beth Pietrak, Nandan Haloi, Yanting Yin, Gary John Tresadern, Laura Perez-Benito, Erik Lindahl, Astrid Bottelbergs, Daniel Oehlrich, Nina Van Opdenbosch, Sujata Sharma
February, 2024 In Nature Communications
Structural basis for the oligomerization-facilitated NLRP3 activation
Structural basis for the oligomerization-facilitated NLRP3 activation
DOI
Nandan Haloi, Shan Huang, Aaron L. Nichols, Eve J. Fine, Nicholas J. Friesenhahn, Christopher B. Marotta, Dennis A Dougherty, Erik Lindahl, Rebecca J. Howard, Stephen L. Mayo, Henry A. Lester
February, 2024 In PEDS
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids
Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids
DOI
John Cowgill, Chen Fan, Nandan Haloi, Victor Tobiasson, Yuxuan Zhuang, Rebecca J Howard, Erik Lindahl
November, 2023 In Neuron
Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor
Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor
DOI
Subhasis Dey, Anjali Patel, Nandan Haloi, Soumya Srimayee, Suman Paul, Ganesh Kumar Barik, Nasim Akhtar, Dipanjan Shaw, Gunanka Hazarika, Biswa Mohan Prusty, Mohit Kumar, Manas Kumar Santra, Emad Tajkhorshid, Surajit Bhattacharjee, Debasis Manna
July, 2023 In J. Med. Chem.
Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity
Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity
DOI
Vasyl Bondarenko, Qiang Chen, Kevin Singewald, Nandan Haloi, Tommy S. Tillman, Rebecca J. Howard, Erik Lindahl, Yan Xu, Pei Tang
February, 2023 In ACS Chem. Neurosci.
Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization
Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization
DOI
Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf, Po-Chao Wen, William W. Metcalf, Paul J. Hergenrother, Diwakar Shukla, Emad Tajkhorshid
February, 2022 In PNAS
Role of internal loop dynamics in antibiotic permeability of outer membrane porins
Role of internal loop dynamics in antibiotic permeability of outer membrane porins
DOI
Nandan Haloi, Archit Kumar Vasan, Emily J. Geddes, Arjun Prasanna, Po-Chao Wen, William W. Metcalf, Paul J. Hergenrother, Emad Tajkhorshid
October, 2021 In Chemical Science
Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge
Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge
DOI
Nandan Haloi, Po-Chao Wen, Qunli Cheng, Meiying Yang, Gayathri Natarajan, Amadou K. S. Camara, Wai-Meng Kwok, Emad Tajkhorshid
June, 2021 In Communications Biology
Structural basis of complex formation between mitochondrial anion channel VDAC1 and Hexokinase-II
Structural basis of complex formation between mitochondrial anion channel VDAC1 and Hexokinase-II
DOI
Sonya Kumar Bharathkar, Benjamin W Parker, Andrey G Malyutin, Nandan Haloi, Kathryn E Huey-Tubman, Emad Tajkhorshid, Beth M Stadtmueller
October, 2020 In eLife
The structures of secretory and dimeric immunoglobulin A
The structures of secretory and dimeric immunoglobulin A
DOI