Search Results - "O’Meara, Matthew J"

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design by Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J

“…Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation…”
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Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2 by Tummino, Tia A, Rezelj, Veronica V, Fischer, Benoit, Fischer, Audrey, O'Meara, Matthew J, Monel, Blandine, Vallet, Thomas, White, Kris M, Zhang, Ziyang, Alon, Assaf, Schadt, Heiko, O'Donnell, Henry R, Lyu, Jiankun, Rosales, Romel, McGovern, Briana L, Rathnasinghe, Raveen, Jangra, Sonia, Schotsaert, Michael, Galarneau, Jean-René, Krogan, Nevan J, Urban, Laszlo, Shokat, Kevan M, Kruse, Andrew C, García-Sastre, Adolfo, Schwartz, Olivier, Moretti, Francesca, Vignuzzi, Marco, Pognan, Francois, Shoichet, Brian K

“…Repurposing drugs as treatments for COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has drawn much attention…”
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Morphological cell profiling of SARS-CoV-2 infection identifies drug repurposing candidates for COVID-19 by Mirabelli, Carmen, Wotring, Jesse W., Zhang, Charles J., McCarty, Sean M., Fursmidt, Reid, Pretto, Carla D., Qiao, Yuanyuan, Zhang, Yuping, Frum, Tristan, Kadambi, Namrata S., Amin, Anya T., O’Meara, Teresa R., Spence, Jason R., Huang, Jessie, Alysandratos, Konstantinos D., Kotton, Darrell N., Handelman, Samuel K., Wobus, Christiane E., Weatherwax, Kevin J., Mashour, George A., O’Meara, Matthew J., Chinnaiyan, Arul M., Sexton, Jonathan Z.

“…The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the associated disease COVID-19, requires therapeutic interventions…”
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A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design by Ó Conchúir, Shane, Barlow, Kyle A, Pache, Roland A, Ollikainen, Noah, Kundert, Kale, O'Meara, Matthew J, Smith, Colin A, Kortemme, Tanja

“…The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for…”
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High-Throughput Screening Identifies Genes Required for Candida albicans Induction of Macrophage Pyroptosis by O'Meara, Teresa R, Duah, Kwamaa, Guo, Cynthia X, Maxson, Michelle E, Gaudet, Ryan G, Koselny, Kristy, Wellington, Melanie, Powers, Michael E, MacAlpine, Jessie, O'Meara, Matthew J, Veri, Amanda O, Grinstein, Sergio, Noble, Suzanne M, Krysan, Damian, Gray-Owen, Scott D, Cowen, Leah E

“…The innate immune system is the first line of defense against invasive fungal infections. As a consequence, many successful fungal pathogens have evolved…”
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The Cryptococcus neoformans Rim101 Transcription Factor Directly Regulates Genes Required for Adaptation to the Host by O'Meara, Teresa R, Xu, Wenjie, Selvig, Kyla M, O'Meara, Matthew J, Mitchell, Aaron P, Alspaugh, J Andrew

“…Classifications Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit…”
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Prediction of enzymatic pathways by integrative pathway mapping by Calhoun, Sara, Korczynska, Magdalena, Wichelecki, Daniel J, San Francisco, Brian, Zhao, Suwen, Rodionov, Dmitry A, Vetting, Matthew W, Al-Obaidi, Nawar F, Lin, Henry, O'Meara, Matthew J, Scott, David A, Morris, John H, Russel, Daniel, Almo, Steven C, Osterman, Andrei L, Gerlt, John A, Jacobson, Matthew P, Shoichet, Brian K, Sali, Andrej

“…The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and…”
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Ultra-large library docking for discovering new chemotypes by Lyu, Jiankun, Wang, Sheng, Balius, Trent E., Singh, Isha, Levit, Anat, Moroz, Yurii S., O’Meara, Matthew J., Che, Tao, Algaa, Enkhjargal, Tolmachova, Kateryna, Tolmachev, Andrey A., Shoichet, Brian K., Roth, Bryan L., Irwin, John J.

“…Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible…”
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Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta by O’Meara, Matthew J, Leaver-Fay, Andrew, Tyka, Michael D, Stein, Amelie, Houlihan, Kevin, DiMaio, Frank, Bradley, Philip, Kortemme, Tanja, Baker, David, Snoeyink, Jack, Kuhlman, Brian

“…Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in…”
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Structures of the σ2 receptor enable docking for bioactive ligand discovery by Alon, Assaf, Lyu, Jiankun, Braz, Joao M., Tummino, Tia A., Craik, Veronica, O’Meara, Matthew J., Webb, Chase M., Radchenko, Dmytro S., Moroz, Yurii S., Huang, Xi-Ping, Liu, Yongfeng, Roth, Bryan L., Irwin, John J., Basbaum, Allan I., Shoichet, Brian K., Kruse, Andrew C.

“…The σ 2 receptor has attracted intense interest in cancer imaging 1 , psychiatric disease 2 , neuropathic pain 3 – 5 and other areas of biology 6 , 7 . Here we…”
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A human liver organoid screening platform for DILI risk prediction by Zhang, Charles J., Meyer, Sophia R., O’Meara, Matthew J., Huang, Sha, Capeling, Meghan M., Ferrer-Torres, Daysha, Childs, Charlie J., Spence, Jason R., Fontana, Robert J., Sexton, Jonathan Z.

“…Drug-induced liver injury (DILI), both intrinsic and idiosyncratic, causes frequent morbidity, mortality, clinical trial failures and post-approval withdrawal…”
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Scientific benchmarks for guiding macromolecular energy function improvement by Leaver-Fay, Andrew, O'Meara, Matthew J, Tyka, Mike, Jacak, Ron, Song, Yifan, Kellogg, Elizabeth H, Thompson, James, Davis, Ian W, Pache, Roland A, Lyskov, Sergey, Gray, Jeffrey J, Kortemme, Tanja, Richardson, Jane S, Havranek, James J, Snoeyink, Jack, Baker, David, Kuhlman, Brian

“…Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and…”
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Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease by Anderson, Faith M, Visser, Noelle D, Amses, Kevin R, Hodgins-Davis, Andrea, Weber, Alexandra M, Metzner, Katura M, McFadden, Michael J, Mills, Ryan E, O'Meara, Matthew J, James, Timothy Y, O'Meara, Teresa R

“…Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C. albicans is remarkably versatile in its ability to…”
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Local delivery of stabilized chondroitinase ABC degrades chondroitin sulfate proteoglycans in stroke-injured rat brains by Hettiaratchi, Marian H., O'Meara, Matthew J., Teal, Carter J., Payne, Samantha L., Pickering, Andrew J., Shoichet, Molly S.

“…Central nervous system (CNS) injuries, such as stroke and spinal cord injuries, result in the formation of a proteoglycan-rich glial scar, which acts as a…”
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Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell by Pulianmackal, Lisa T., Limcaoco, Jose Miguel I., Ravi, Keerthikka, Yang, Sinyu, Zhang, Jeffrey, Tran, Mimi K., Ghalmi, Maria, O’Meara, Matthew J., Vecchiarelli, Anthony G.

“…In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors involved in spatial regulation are…”
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Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets by Fu, Ci, Zhang, Xiang, Veri, Amanda O., Iyer, Kali R., Lash, Emma, Xue, Alice, Yan, Huijuan, Revie, Nicole M., Wong, Cassandra, Lin, Zhen-Yuan, Polvi, Elizabeth J., Liston, Sean D., VanderSluis, Benjamin, Hou, Jing, Yashiroda, Yoko, Gingras, Anne-Claude, Boone, Charles, O’Meara, Teresa R., O’Meara, Matthew J., Noble, Suzanne, Robbins, Nicole, Myers, Chad L., Cowen, Leah E.

“…Fungal pathogens pose a global threat to human health, with Candida albicans among the leading killers. Systematic analysis of essential genes provides a…”
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CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair by O'Meara, Matthew J, Rapala, Jackson R, Nichols, Connie B, Alexandre, A Christina, Billmyre, R Blake, Steenwyk, Jacob L, Alspaugh, J Andrew, O'Meara, Teresa R

“…Elucidating gene function is a major goal in biology, especially among non-model organisms. However, doing so is complicated by the fact that molecular…”
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The Recognition of Identical Ligands by Unrelated Proteins by Barelier, Sarah, Sterling, Teague, O’Meara, Matthew J, Shoichet, Brian K

“…The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands…”
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The life and times of endogenous opioid peptides: Updated understanding of synthesis, spatiotemporal dynamics, and the clinical impact in alcohol use disorder by Margolis, Elyssa B., Moulton, Madelyn G., Lambeth, Philip S., O'Meara, Matthew J.

“…The opioid G-protein coupled receptors (GPCRs) strongly modulate many of the central nervous system structures that contribute to neurological and psychiatric…”
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Imaging-Based Screening Identifies Modulators of the eIF3 Translation Initiation Factor Complex in Candida albicans by Metzner, Katura, O'Meara, Matthew J, Halligan, Benjamin, Wotring, Jesse W, Sexton, Jonathan Z, O'Meara, Teresa R

“…Fungal pathogens like Candida albicans can cause devastating human disease. Treatment of candidemia is complicated by the high rate of resistance to common…”
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