|
| 319. VMD as a platform for interactive small molecule preparation and
visualization in quantum and classical simulations.
Mariano Spivak, John E. Stone, Jo ao Ribeiro, Jan Saam, Peter L. Freddolino,
Rafael C. Bernardi, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 63:4664-4678,
2023.
Published.
|
| 318. Quinoline thiourea-based zinc ionophores with antibacterial activity.
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, and Debasis Manna.
Journal of Medicinal Chemistry, 66:11078-11093, 2023.
Published.
|
| 317. Application experiences on a gpu-accelerated arm-based hpc testbed.
Wael Elwasif, William Godoy, Nick Hagerty, J. Austin Harris, Oscar Hernandez,
Balint Joo, Paul Kent, Damien Lebrun-Grandie, Elijah Maccarthy,
Veronica Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei
Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan,
Rene Widera, Spencer Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey
Young, Sunita Chandrasekaran, Florina Ciorba, Osman Simsek, Kate Clark,
Filippo Spiga, Jeff Hammond, John Stone, David Hardy, Sebastian Keller,
Jean-Guillaume Piccinali, and Christian Trott.
In Proceedings of the HPC Asia 2023 Workshops, HPC Asia '23
Workshops, pp. 35-49, New York, NY, USA, 2023. Association for Computing
Machinery.
|
| 316. Structures and membrane interactions of native serotonin transporter
in complexes with psychostimulants.
Dongxue Yang, Zhiyu Zhao, Emad Tajkhorshid, and Eric Gouaux.
Proceedings of the National Academy of Sciences, USA,
120:e2304602120, 2023.
Published.
|
| 315. End-to-end AI framework for interpretable prediction of molecular
and crystal properties.
Hyun Park, Ruijie Zhu, E. A. Huerta, Santanu Chaudhuri, Emad Tajkhorshid, and
Donny Cooper.
Machine Learning: Science and Technology, 4:025036, 2023.
Published.
|
| 314. Insights into substrate transport and water permeation in the
mycobacterial transporter MmpL3.
Yupeng Li, Atanu Acharya, Lixinhao Yang, Jinchan Liu, Emad Tajkhorshid,
Helen I. Zgurskaya, Mary Jackson, and James C. Gumbart.
Biophysical Journal, 122:2342-2352, 2023.
Published.
(PMC: PMC10257117) |
| 313. Tuning phenylalanine fluorination to assess aromatic contributions to
protein function and stability in cells.
Grace D. Galles, Daniel T. Infield, Colin J. Clark, Marcus L. Hemshorn, Shivani
Manikandan, Frederico Fazan, Ali Rasouli, Emad Tajkhorshid, Jason D. Galpin,
Richard B. Cooley, Ryan A. Mehl, and Christopher A. Ahern.
Nature Communications, 14, 2023.
Published.
(PMC: PMC9813137) |
| 312. #COVIDisAirborne: AI-enabled multiscale computational microscopy
of delta SARS-CoV-2 in a respiratory aerosol.
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer,
Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda
Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra
Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa
Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith,
Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick Manby, Anima
Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David
Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher
Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard
Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas
Miller, Shantenu Jha, Arvind Ramanathan, Lillian Chong, and Rommie Amaro.
The International Journal of High Performance Computing
Applications, 37:10943420221128233, 2022.
(PMC: PMC8609898) |
| 311. Differential interactions of selected phytocannabinoids with human
CYP2D6 polymorphisms.
Hannah C. Huff, Archit Vasan, Pritam Roy, Aayush Kaul, Emad Tajkhorshid, and
Aditi Das.
Biochemistry, 60:2749-2760, 2021.
(PMC: PMC8455456) |
| 310. Backbone amides are key determinants of Cl− selectivity in
CLC ion channels.
Lilia Leisle, Kin Lam, Sepehr Dehghani-Ghahnaviyeh, Eva Fortea, Jason Galpin,
Christopher A. Ahern, Emad Tajkhorshid, and Alessio Accardi.
Nature Communications, 13, 2022.
Published.
(PMC: PMC9726985) |
| 309. Cryo-EM structures of human ABCA7 provide insights into its
phospholipid translocation mechanisms.
Le Thi My Le, James R. Thompson, Sepehr Dehghani-Ghahnaviyeh, Shashank Pant,
Phuoc X. Dang, Takahisa Kanikeyo, Emad Tajkhorshid, and Amer Alam.
EMBO Journal, 42:e111065, 2023.
(PMC: PMC9890230) |
| 308. Differential dynamics and direct interaction of bound ligands with
lipids in multidrug transporter ABCG2.
Ali Rasouli, Qin Yu, Sepehr Dehghani-Ghahnaviyeh, Po-Chao Wen, Julia Kowal,
Kaspar Lochar, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
120:e2213437120, 2022.
Published.
|
| 307. Lipid-mediated prestin organization in outer hair cell membranes and
its implications in sound amplification.
Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, and Emad Tajkhorshid.
Nature Communications, 13, 2022.
(PMC: PMC9653410) |
| 306. Molecular view into preferential binding of the factor VII gla
domain to phosphatidic acid.
Melanie P. Muller, James H. Morrissey, and Emad Tajkhorshid.
Biochemistry, 61:1694-1703, 2022.
|
| 305. Structures of the TMC-1 complex illuminate mechanosensory
transduction.
H. Jeong, S. Clark, A. Goehring, Sepehr Dehghani-Ghahnaviyeh, Ali Rasouli, Emad
Tajkhorshid, and Eric Gouaux.
Nature, 610:796-803, 2022.
(PMC: PMC9605866) |
| 304. Proton-driven alternating access in a spinster lipid transporter.
Reza Dastvan, Ali Rasouli, Sepehr Dehghani-Ghahnaviyeh, Samantha Gies, and Emad
Tajkhorshid.
Nature Communications, 13, 2022.
|
| 303. Targeting lipid-protein interaction to treat Syk-mediated acute
myeloid leukemia.
I. Singaram, A. Sharma, S. Pant, M. Lihan, M.-J. Park, P. Buwaneka, Y. Hu,
N. Mahmud, Y.-M. Kim, V. Gevorgyan, I. Khan, Emad Tajkhorshid, and W. Cho.
Nature Chemical Biology, 19:239-250, 2023.
Published.
(PMC: PMC9898191) |
| 302. py-MCMD: Python software for performing hybrid monte
carlo/molecular dynamics simulations with GOMC and NAMD.
Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy,
John E. Stone, Loren Schwiebert, Jeffrey Potoff, and Emad Tajkhorshid.
Journal of Chemical Theory and Computation, 18:4983-4994,
2022.
|
| 301. Phthalate monoesters act through peroxisome proliferator-activated
receptors in the mouse ovary.
Daryl D. Meling, Kathy M. De La Torre, Andres S. Arango, Andressa Gonsioroski,
Ashley R. K. Deviney, Alison M. Neff, Mary J. Laws, Genoa R. Warner, Emad
Tajkhorshid, and Jodi A. Flaws.
Reproductive Toxicology, 110:113-123, 2022.
|
| 300. ANARI: A 3-D rendering API standard.
J. E. Stone, K. Griffin, J. Amstutz, D. DeMarle, W. Sherman, and
J. Günther.
Computing in Science and Engineering, 24:7-18, 2022.
|
| 299. Posttranslational modifications optimize the ability of SARS-CoV-2
spike for effective interaction with host cell receptors.
Karan Kapoor, Tianle Chen, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
119:e2119761119, 2022.
(PMC: PMC9282386) |
| 298. Extended-ensemble docking to probe dynamic variation of ligand
binding sites during large-scale structural changes of proteins.
Karan Kapoor, Sundar Thangapandian, and Emad Tajkhorshid.
Chemical Science, 13:4150-4169, 2022.
(PMC: PMC8985516) |
| 297. Experiences porting NAMD to the Data Parallel C++ programming
model.
David J. Hardy, Jaemin Choi, Wei Jiang, and Emad Tajkhorshid.
In International Workshop on OpenCL, IWOCL'22, New York, NY,
USA, 2022. Association for Computing Machinery.
|
| 296. Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel
activity and glial regulation of CNS function.
Qianyi Wu, Azman Akhter, Shashank Pant, Eunjoo Cho, Jin Xin Zhu, Alastair R
Garner, Tomoko Ohyama, Emad Tajkhorshid, Donald J van Meyel, and Renae M
Ryan.
Journal of Clinical Investigation, 132:e154891, 2022.
(PMC: PMC8970671) |
| 295. Use of microscale thermophoresis to measure protein-lipid
interactions.
Robert P. Sparks, William Lawless, Andres S. Arango, Emad Tajkhorshid, and
Rutilio A. Fratti.
Journal of Visualized Experiments, 180, 2022.
|
| 294. Microscopic characterization of the chloride permeation pathway in
the human excitatory amino acid transporter 1 (EAAT1).
Shashank Pant, Qianyi Wu, Renae Ryan, and Emad Tajkhorshid.
ACS Chemical Neuroscience, 13:776-785, 2022.
|
| 293. Identification of structural transitions in bacterial fatty acid
binding proteins that permit ligand entry and exit at membranes.
Jessica M. Gullett, Maxime G. Cuypers, Christy R. Grace, Shashank Pant, Chitra
Subramanian, Emad Tajkhorshid, Charles O. Rock, and Stephen W. White.
Journal of Biological Chemistry, 298:101676, 2022.
(PMC: PMC8892158) |
| 292. A companion guide to the string method with swarms of trajectories:
Characterization, performance, and pitfalls.
Haochuan Chen, Dylan Ogden, Shashank Pant, Wensheng Cai, Emad Tajkhorshid,
Mahmoud Moradi, Benoit Roux, and Christophe Chipot.
Journal of Chemical Theory and Computation, 18:1406-1422,
2022.
|
| 291. Intelligent resolution: Integrating cryo-EM with AI-driven
multi-resolution simulations to observe the SARS-CoV-2
replication-transcription machinery in action.
Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim
Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei
Huang, John McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis
Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey
Wells, Venkatesh Mysore, Thomas Gibbs, James Phillips, S. Chakra
Chennubhotla, Ian Foster, Rick Stevens, Anima Anandkumar, Venkatram
Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, and Arvind
Ramanathan.
The International Journal of High Performance Computing
Applications, 36:603-623, 2022.
|
| 290. Role of internal loop dynamics in antibiotic permeability of outer
membrane porins.
Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf,
Po-Chao Wen, William W. Metcalf, Paul J. Hergenrother, Diwakar Shukla, and
Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
119:e2117009119, 2022.
(PMC: PMC8872756) |
| 289. Anthracycline derivatives inhibit cardiac CYP2J2.
Justin S. Kim, Andres S. Arango, Swapnil Shah, William R Arnold, Emad
Tajkhorshid, and Aditi Das.
Journal of Inorganic Biochemistry, 229:111722, 2022.
(PMC: PMC8860876) |
| 288. Anionic lipids confine cytochrome c2 to the surface of
bioenergetic membranes without compromising its interaction with redox
partners.
Chun Kit Chan, Abhishek Singharoy, and Emad Tajkhorshid.
Biochemistry, 61:385-397, 2022.
|
| 287. Membrane Mixer: A toolkit for efficient shuffling of lipids in
heterogeneous biological membranes.
Giuseppe Licari, Sepehr Dehghani-Ghahnaviyeh, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 62:986-996,
2022.
|
| 286. Assembly and analysis of cell-scale membrane envelopes.
Josh Vermaas, Chris Mayne, Eric Shinn, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 62:602-617,
2022.
(PMC: PMC8903035) |
| 285. Lessons learned from responsive molecular dynamics studies of the
COVID-19 virus.
David J. Hardy, John E. Stone, Barry Isralewitz, and Emad Tajkhorshid.
IEEE/ACM HPC for Urgent Decision Making 2021, pp. 1-10,
2021.
|
| 284. ChAdOx1 interacts with CAR and PF4 with implications for
thrombosis with thrombocytopenia syndrome.
Alexander T. Baker, Ryan J. Boyd, Daipayan Sarkar, John Vant, Alicia Teijeira
Crespo, Chloe D. Truong, Emily Bates, Eric Wilson, Chun Kit Chan, Magdalena
Lipka-Lloyd, Petra Fromme, Marius Bolni Nagalo, Meike Heurich, Dewight
Williams, Po-Lin Chiu, Pierre J. Rizkallah, Alan L. Parker, Abhishek
Singharoy, and Mitesh J. Borad.
Science Advances, 7:eabl8213, 2021.
|
| 283. Cryo-EM structures of Escherichia coli cytochrome
bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic
substrate binding site.
Jiao Li, Long Han, Francesca Vallese, Ziqiao Ding, Sylvia K. Choi, Sangjin
Hong, Yanmei Luo, Bin Liu, Chun Kit Chan, Emad Tajkhorshid, Jiapeng Zhu,
Oliver Clarke, Kai Zhang, and Robert Gennis.
Proceedings of the National Academy of Sciences, USA,
118:e2106750118, 2021.
(PMC: PMC8403832) |
| 282. PIP2-dependent coupling of voltage sensor and pore domains in
Kv7.2.
Shashank Pant, Jiaren Zhang, Eung Kim, Kin Lam, Hee Jung Chung, and Emad
Tajkhorshid.
Communications Biology, 4, 2021.
|
| 281. Rationalizing generation of broad spectrum antibiotics with the
addition of a positive charge.
Nandan Haloi, Archit Kumar Vasan, Emily Jane Geddes, Arjun Prasanna, Po-Chao
Wen, William W. Metcalf, Paul J Hergenrother, and Emad Tajkhorshid.
Chemical Science, 12:15028-15044, 2021.
|
| 280. Molecular mechanism of capsid disassembly in hepatitis B virus.
Zhaleh Ghaemi, Martin Gruebele, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
118:e2102530118, 2021.
|
| 279. Molecular mechanism of prestin electromotive signal amplification.
Jingpeng Ge, Johannes Elferich, Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, Marc
Meadows, Henrique von Gersdorff, Emad Tajkhorshid, and Eric Gouaux.
Cell, 184:4669-4679, 2021.
|
| 278. CryoFold: Determining protein structures and data-guided ensembles
from cryo-EM density maps.
M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, J. Nguyn, N. J. Sisco, A. Mondal,
J. Vant, P. Fromme, W. D. Van Horn, Emad Tajkhorshid, D. Kihara, K. Dill,
A. Perez, and A. Singharoy.
Matter, 4:3195-3216, 2021.
|
| 277. Editorial: Mitochondrial exchangers and transporters in cell survival
and death.
Amadou K. S. Camara Wai-Meng Kwok, Emad Tajkhorshid.
Frontiers in Physiology, 12:1415, 2021.
|
| 276. Defining the energetic basis for a conformational switch mediating
ligand-independent activation of mutant estrogen receptors in breast cancer.
Chris Mayne, W. Toy, K. Carlson, T. Bhatt, S. W. Fanning, G. L. Greene, B. S.
Katzenellenbogen, S. Chandarlapaty, J. A. Katzenellenbogen, and Emad
Tajkhorshid.
Molecular Cancer Research, 19:1559-1570, 2021.
|
| 275. Structural basis of complex formation between mitochondrial anion
channel VDAC1 and hexokinase-II.
Nandan Haloi, Po-Chao Wen, Qunli Cheng, Meiying Yang, Gayathri Natarajan,
Amadou KS Camara, Wai-Meng Kwok, and Emad Tajkhorshid.
Communications Biology, 4:667, 2021.
|
| 274. Calmodulin complexes with brain and muscle creatine kinase peptides.
Janina Sprenger, Anda Trifan, Neal Patel, Ashley Vanderbeck, Jenny Bredtfelt,
Emad Tajkhorshid, Roger Rowlett, Leila Lo Leggio, Karin S. Åkerfeldt, and
Sara Linse.
Current Research in Structural Biology, 3:121-132, 2021.
|
| 273. Active participation of membrane lipids in inhibition of multidrug
transporter P-glycoprotein.
Karan Kapoor, Shashank Pant, and Emad Tajkhorshid.
Chemical Science, 12:6293-6306, 2021.
|
| |
| 271. Cation-π interactions and their functional roles in membrane
proteins.
Daniel T. Infield, Ali Rasouli, Grace G. Galles, Christophe Chipot, Emad
Tajkhorshid, and Christopher A. Ahern.
Journal of Molecular Biology, 433:167035, 2021.
(PMC: PMC8338773) |
| 270. Structural insights into photosystem II assembly.
Jure Zabret, Stefan Bohn, Sandra K. Schuller, Oliver Arnolds, Madeline
Möller, Jakob Meier-Credo, Pasqual Liauw, Aaron Chan, Emad Tajkhorshid,
Julian D. Langer, Raphael Stoll, Anja Krieger-Liszkay, Benjamin D. Engel,
Till Rudack, Jan M. Schuller, and Marc M. Nowaczyk.
Nature Plants, 7:524-538, 2021.
|
| 269. Multilevel summation for periodic electrostatics using B-splines.
Hüseyin Kaya, David J. Hardy, and Robert D. Skeel.
Journal of Chemical Physics, 154:144105, 2021.
(PMC: PMC8036131) |
| 268. Classical molecular dynamics.
Charles L. Brooks III, David A. Case, Steve Plimpton, Benoit Roux, David
van der Spoel, and Emad Tajkhorshid.
Journal of Chemical Physics, 154:10041, 2021.
|
| 267. Binding mode of SARS-CoV2 fusion peptide to human cellular
membrane.
Defne Gorgun, Muyun Lihan, Karan Kapoor, and Emad Tajkhorshid.
Biophysical Journal, 120:191a, 2021.
|
| 266. Mechanical properties of ester- and ether-DPhPC bilayers: a
molecular dynamics study.
Ali Rasouli, Yousef Jamali, Emad Tajkhorshid, Omid Bavi, and Hossein Nejat
Pishkenari.
Journal of the Mechanical Behavior of Biomedical Materials,
117:104386, 2021.
(PMC: PMC8009841) |
| 265. Amphiphilic distyrylbenzene derivatives as potential therapeutic and
imaging agents for the soluble amyloid-β oligomers in alzheimer's
disease.
Liang Sun, Hong-Jun Cho, Soumyo Sen, Andres S. Arango, Truc T. Huynh, Yiran
Huang, Nilantha Bandara, Buck E. Rogers, Emad Tajkhorshid, and Liviu M.
Mirica.
Journal of the American Chemical Society, 143:10462-10476,
2021.
(PMC: PMC8762579) |
| 264. Glutamate transporters have a chloride channel with two hydrophobic
gates.
Ichia Chen, Shashank Pant, Qianyi Wu, Rosemary Cater, Meghna Sobti, Robert
Vandenberg, Alastair G. Stewart, Emad Tajkhorshid, Josep Font, and Renae
Ryan.
Nature, 591:327-331, 2021.
|
| 263. Carbon dioxide transport across membranes.
Marie Michenkova, Sara Taki, Matthew C. Blosser, Hyea J. Hwang, Thomas Kowatz,
Fraser J. Moss, Rossana Occhipinti, Xue Qin, Soumyo Sen, Eric Shinn, Dengke
Wang, Brian S. Zeise, Pan Zhao, Noah Malmstadt, Ardeschir Vahedi-Faridi, Emad
Tajkhorshid, and Walter F. Boron.
Interface Focus, 11:20200090, 2021.
|
| 262. Theoretical description of the primary proton-coupled electron
transfer reaction in the cytochrome bc1 complex.
Angela M. Barragan, Alexander V. Soudackov, Zaida Luthey-Schulten, Sharon
Hammes-Schiffer, Klaus Schulten, and Ilia A. Solov'yov.
Journal of the American Chemical Society, 143:715-723, 2021.
|
| 261. Multiscale modeling and cinematic visualization of photosynthetic
energy conversion processes from electronic to cell scales.
Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz,
Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida
Luthey-Schulten, and Donna Cox.
Parallel Computing, 102:102698, 2021.
|
| 260. Anti-inflammatory dopamine- and serotonin-based endocannabinoid
epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel.
William R. Arnold, Lauren N. Carnevale, Zili Xie, Javier L. Baylon, Emad
Tajkhorshid, Hongzhen Hu, and Aditi Das.
Nature Communications, 12, 2021.
|
| 259. Confronting pitfalls of AI-augmented molecular dynamics using
statistical physics.
Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, and Pratyush
Tiwary.
Journal of Chemical Physics, 153, 2020.
|
| 258. Scalable analysis of authentic viral envelopes on FRONTERA.
Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla,
and Juan R. Perilla.
Computing in Science and Engineering, 22:11-20, 2020.
|
| |
| 256. The structures of secretory and dimeric immunoglobulin A.
Sonya Kumar Bharathkar, Benjamin W Parker, Andrey G Malyutin, Nandan Haloi,
Kathryn E Huey-Tubman, Emad Tajkhorshid, and Beth Stadtmueller.
eLife, 9:e56098, 2020.
(PMC: PMC7707832) |
| 255. Hydrogen-deuterium exchange mass spectrometry captures distinct
dynamics upon substrate and inhibitor binding to a transporter.
Ruyu Jia, Chloe Martens, Mrinal Shekhar, Shashank Pant, Grant Pellowe, Andy
Lau, Heather Findlay, Nicola Harris, Emad Tajkhorshid, Paula Booth, and
Argyris Politis.
Nature Communications, 11, 2020.
(PMC: PMC7710758) |
| 254. Parameterization of a drug molecule with a halogen σ-hole
particle using ffTK: Implementation, testing, and comparison.
Yui Tik Pang, Anna Pavlova, Emad Tajkhorshid, and James C. Gumbart.
Journal of Chemical Physics, 153:164104, 2020.
|
| 253. Structural basis for the reaction cycle of DASS dicarboxylate
transporters.
David B Sauer, Noah Trebesch, Jennifer J Marden, Nicolette Cocco, Jinmei Song,
Akiko Koide, Shohei Koide, Emad Tajkhorshid, and Da-Neng Wang.
eLife, 9:e61350, 2020.
(PMC: PMC7553777) |
| 252. Benchmarking machine learning workloads in structural bioinformatics
applications.
Heng Ma, Austin Clyde, Anda Trifan, Venkatram Vishwanath, Arvind Ramanathan,
Debsindhu Bhowmik, and Shantenu Jha.
First International Workshop on Benchmarking Machine Learning
Workloads on Emerging Hardware: CHALLENGE20, 2020.
|
| 251. Membrane surface recognition by the ASAP1 PH domain and
consequences for interactions with the small GTPase Arf1.
O. Soubias, Shashank Pant, F. Heinrich, N. S. Roy Y. Zhang, J. Li, X. Jian,
M. E Yohe, P. A. Randazzo, M. Lösche, Emad Tajkhorshid, and R. A. Byrd.
Science Advances, 6, 2020.
(PMC: PMC7527224) |
| 250. Structural and functional diversity calls for a new classification of
ABC transporters.
Christoph Thomas, Stephen G. Aller, Konstantinos Beis, Elisabeth P. Carpenter,
Geoffrey Chang, Lei Chen, Elie Dassa, Michel Dean, Franck Duong Van Hoa,
Damian Ekiert, Robert Ford, Rachelle Gaudet, Xin Gong, I. Barry Holland,
Yihua, Vassilis Koronakis, Christopher M. Koth, Youngsook Lee, Oded Lewinson,
Roland Lill, Enrico Martinoia, Satoshi Murakami, Heather W. Pinket, Bert
Poolman, Daniel Rosenbaum, Balazs Sarkadi, Lutz Schmitt, Erwin Schneider,
Yigong Shi, Show-Ling Shyng, Dirk J. Slotboom, Emad Tajkhorshid,
Kazumitsu Ueda D. Peter Tieleman, Andras Varadi, Po-Chao Wen, Nieng Yan, Peng
Zhang, Hongjin Zheng, Jochen Zimmer, and Robert Tampe.
FEBS Letters, 594:3767-3775, 2020.
|
| 249. Boosting free-energy perturbation calculations with GPU-accelerated
NAMD.
Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai,
Christophe Chipot, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 60:5301-5307,
2020.
(PMC: PMC7686227) |
| 248. Knockout of VDAC1 in H9c2 cells promotes oxidative stress-induced
cell apoptosis through decreased mitochondrial hexokinase II binding and
enhanced glycolytic stress.
Meiying Yang, Jie Sun, David F Stowe, Emad Tajkhorshid, Wai-Meng Kwok, and
Amadou KS Camara.
Cellular Physiology & Biochemistry, 54:853-874, 2020.
Published.
|
| 247. Scalable molecular dynamics on CPU and GPU architectures with
NAMD.
James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone,
João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin,
Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo,
Brian Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux,
Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé, Klaus
Schulten, Christophe Chipot, and Emad Tajkhorshid.
Journal of Chemical Physics, 153:044130, 2020.
(PMC: PMC7395834) |
| 246. Aquaporin-7: A dynamic aquaglyceroporin with higher water and
glycerol transport capacity than its bacterial homolog GlpF.
Fraser J Moss, Paween Mahinthichaichan, David T Lodowski, Thomas Kowatz, Emad
Tajkhorshid, Andreas Engel, Walter F Boron, and Ardeshir Vahedi-Faridi.
Frontiers in Physiology, 11, 2020.
Published.
(PMC: PMC7339978) |
| 245. Membrane interactions of Cy3/Cy5 fluorophores and their effects on
membrane protein dynamics.
Kin Lam and Emad Tajkhorshid.
Biophysical Journal, 119:24-34, 2020.
(PMC: PMC7335937) |
| 244. Aβ(1-42) tetramer and octamer structures reveal edge
conductivity pores as a mechanism for membrane damage.
Sonia Ciudad, Eduard Puig, Thomas Botzanowski, Moeen Meigooni, Andres S.
Arango, Jimmy Do, Maxim Mayzel, Mariam Bayoumi, Stéphane Chaignepain,
Giovanni Maglia, Sarah Cianferani, Vladislav Orekhov, Emad Tajkhorshid,
Benjamin Bardiaux, and Natàlia Carulla.
Nature Communications, 11, 2020.
(PMC: PMC7296003) |
| 243. Twisting and tilting of a mechanosensitive molecular probe detects
order in membranes.
Giuseppe Licari, Karolina Strakova, Stefan Matile, and Emad Tajkhorshid.
Chemical Science, 11:5637-5649, 2020.
(PMC: PMC7433777) |
| 242. Molecular insights into the loading and dynamics of doxorubicin on
PEGylated graphene oxide nanocarriers.
Mina Mahdavi, Ali Fattahi, Emad Tajkhorshid, and Sasan Nouranian.
ACS Applied Bio Materials, 3:1354-1363, 2020.
(PMC: PMC7731932) |
| 241. Menthol binding to the human α4β2 nicotinic
acetylcholine receptor, facilitated by its strong partitioning in membrane.
Rezvan Shahoei and Emad Tajkhorshid.
Journal of Physical Chemistry B, 124:1866-1880, 2020.
(PMC: PMC7094167) |
| 240. Identifying mutation hotspots reveals pathogenetic mechanisms of
KCNQ2 epileptic encephalopathy.
Jiaren Zhang, Eung Chang Kim, Congcong Chen, Erik Procko, Shashank Pant, Kin
Lam, Jaimin Patel, Rebecca Choi, Mary Hong, Dhruv Joshi, Eric Bolton, Emad
Tajkhorshid, and Hee Jung Chung.
Scientific Reports, 10:4756, 2020.
(PMC: PMC7075958) |
| 239. Aberrant expression of a non-muscle RBFOX2 isoform triggers cardiac
conduction defects in myotonic dystrophy.
Chaitali Misra, Sushant Bangru, Feikai Lin, Kin Lam, Sara N. Koenig, Ellen R.
Lubbers, Jamila Hedhli, Nathaniel P. Murphy, Darren J. Parker, Lawrence W.
Dobrucki, Thomas A. Cooper, Emad Tajkhorshid, Peter J. Mohler, and Auinash
Kalsotra.
Developmental Cell, 52:748-763, 2020.
(PMC: PMC7098852) |
| 238. An activity-based sensing approach for the detection of
cyclooxygenase-2 in live cells.
Anuj K. Yadav, Christopher J. Reinhardt, Andres S. Arango, Hannah C. Huff,
Liang Dong, Michael G. Malkowski, Aditi Das, Emad Tajkhorshid, and Jefferson
Chan.
Angewandte Chemie - International Edition in English,
132:2-10, 2019.
|
| 237. In situ conformational changes of the Escherichia coli serine
chemoreceptor in different signaling states.
Wen Yang, Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten,
Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel.
Molecular Biology and Physiology, 10:e00973-19, 2019.
(PMC: PMC6606802) |
| 236. Structure and dynamics of the E. coli chemotaxis core
signaling complex by cryo-electron tomography and molecular simulations.
C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S.
Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang.
Communications Biology, 3:24, 2020.
(PMC: PMC6954272) |
| 235. A CLC-ec1 mutant reveals global conformational change and suggests
a unifying mechanism for the Cl-/H+ transport cycle.
Tanmay S. Chavan, Ricky C. Cheng, Tao Jiang, Irimpan I. Mathews, Richard A.
Stein, Antoine Koehl, Hassane S. Mchaourab, Emad Tajkhorshid, and Merritt
Maduke.
eLife, 9:e53479, 2020.
(PMC: PMC7253180) |
| 234. Streptavidin/biotin: Tethering geometry defines unbinding mechanics.
Steffen M. Sedlak, Leonard C. Schendel, Hermann E. Gaub, and Rafael C.
Bernardi.
Science Advances, 6:eaay5999, 2020.
|
| 233. Mechanisms of nanonewton mechanostability in a protein complex
revealed by molecular dynamics simulations and single-molecule force
spectroscopy.
Rafael C. Bernardi, Ellis Durner, Constantin Schoeler, Klara H. Malinowska,
Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub,
and Michael A. Nash.
Journal of the American Chemical Society, 141:14752-14763,
2019.
(PMC: PMC6939381) |
| 232. Locking two rigid-body bundles in an outward-facing conformation: A
general ion-coupling mechanism in LeuT-fold transporters.
Jing Li, Zhiyu Zhao, and Emad Tajkhorshid.
Scientific Reports, 9:19479, 2019.
(PMC: PMC6925253) |
| 231. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion
channel embedded in a phosphatidylcholine-only bilayer.
Pramod Kumar, Yuhang Wang, Zhening Zhang, Zhiyu Zhao, Gisela D. Cymes, Emad
Tajkhorshid, and Claudio Grosman.
Proceedings of the National Academy of Sciences, USA,
117:1788-1798, 2020.
(PMC: PMC6983364) |
| 230. Atoms to phenotypes: Molecular design principles of cellular energy
metabolism.
A. Singharoy, C. Maffeo, K. Delgardo, D. J. K. Swainsbury, M. Sener,
U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. Stone,
J. Phillips, T. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten,
P. Tieleman, C. N. Hunter, Emad Tajkhorshid, A. Aksimentiev, and K. Schulten.
Cell, 179:1098-1111, 2019.
|
| 229. Binding partner- and force-promoted changes in αE-catenin
conformation probed by native cysteine labeling.
Ksenia Terekhova, Sabine Pokutta, Yee S. Kee, Jing Li, Emad Tajkhorshid, Gerald
Fuller, Alexander R. Dunn, and William I. Weis.
Scientific Reports, 9:15375, 2019.
(PMC: PMC6814714) |
| 228. Federating structural models and data: Outcomes from a workshop on
archiving integrative structures.
Helen M. Berman, Paul D. Adams, Alexandre A. Bonvin, Stephen K. Burley, Bridget
Carragher, Wah Chiu, Frank DiMaio, Thomas E. Ferrin, Margaret J. Gabanyi,
Thomas D. Goddard, Patrick R. Griffin, Juergen Haas, Christian A. Hanke,
Jeffrey C. Hoch, Gerhard Hummer, Genji Kurisu, Catherine L. Lawson, Alexander
Leitner, John L. Markley, Jens Meiler, Gaetano T. Montelione, George
N. Phillips Jr., Thomas Prisner, Juri Rappsilber, David C. Schriemer, Torsten
Schwede, Claus A.M. Seidel, Timothy S. Strutzenberg, Dmitri I. Svergun, Emad
Tajkhorshid, Jill Trewhella, Brinda Vallat, Sameer Velankar, Geerten W.
Vuister, Benjamin Webb, John D. Westbrook, Kate L. White, and Andrej Sali.
Structure, 27:1745-1759, 2019.
|
| 227. Microscopic characterization of GRP1 PH domain interaction with
anionic membranes.
Shashank Pant and Emad Tajkhorshid.
Journal of Computational Chemistry, 41:489-499, 2020.
(PMC: PMC7000246) |
| 226. High-performance analysis of biomolecular containers to measure
small-molecule transport, transbilayer lipid diffusion, and protein cavities.
Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, and Juan R. Perilla.
Journal of Chemical Information and Modeling, 59:4328-4338,
2019.
(PMC: PMC6817393) |
| 225. Tuning symmetry breaking charge separation in perylene bichromophores
by conformational control.
Alexander Aster, Giuseppe Licari, Francesco Zinna, Elodie Brun, Tatu
Kumpulainen, Emad Tajkhorshid, Jerome Lacour, and Eric Vauthey.
Chemical Science, 10:10629-10639, 2019.
|
| 224. Multivalent polymer-peptide conjugates: A general platform for
inhibiting amyloid beta peptide aggregation.
Xing Jiang, Abigail J. Halmes, Giuseppe Licari, John W. Smith, Yang Song,
Edwin G. Moore, Qian Chen, Emad Tajkhorshid, Chad M. Rienstra, and Jeffrey S.
Moore.
ACS Macro Letters, 8:1365-1371, 2019.
(PMC: PMC7059649) |
| 223. Polymer-peptide conjugates convert amyloid into protein nanobundles
through fragmentation and lateral association.
John W. Smith, Xing Jiang, Hyosung An, Alexander M. Barclay, Giuseppe Licari,
Emad Tajkhorshid, Edwin G. Moore, Chad M. Rienstra, Jeffrey S. Moore, and
Qian Shen.
ACS Applied Materials and Interfaces, 3:937-945, 2020.
(PMC: PMC7059651) |
| 222. A chalcogen-bonding cascade switch for planarizable push-pull probes.
Mariano Macchione, Antoine Goujon, Karolina Strakova, Heorhii V. Humeniuk,
Giuseppe Licari, Emad Tajkhorshid, Naomi Sakai, and Stefan Matile.
Angewandte Chemie - International Edition in English,
58:15752-15756, 2019.
(PMC: PMC7035594) |
| 221. Probing cholesterol binding and translocation in P-glycoprotein.
Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1862:183090,
2020.
(PMC: PMC6934093) |
| 220. A small-molecule competitive inhibitor of phosphatidic acid binding
by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole
fusion.
Robert P. Sparks, Andres S. Arango, Matthew L. Starr, Zachary L. Aboff,
Logan R. Hurst, David A. Rivera-Kohr, Chi Zhang, Kevin A. Harden, Jermaine L.
Jenkins, Wayne C. Guida, Emad Tajkhorshid, and Rutilio A. Fratti.
Journal of Biological Chemistry, 294:17168-17185, 2019.
(PMC: PMC6873166) |
