Search Results - "Kretsch, Rachael"

Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms by Billesbølle, Christian B., Azumaya, Caleigh M., Kretsch, Rachael C., Powers, Alexander S., Gonen, Shane, Schneider, Simon, Arvedson, Tara, Dror, Ron O., Cheng, Yifan, Manglik, Aashish

“…The serum level of iron in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin regulates…”
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RNA target highlights in CASP15: Evaluation of predicted models by structure providers by Kretsch, Rachael C., Andersen, Ebbe S., Bujnicki, Janusz M., Chiu, Wah, Das, Rhiju, Luo, Bingnan, Masquida, Benoît, McRae, Ewan K. S., Schroeder, Griffin M., Su, Zhaoming, Wedekind, Joseph E., Xu, Lily, Zhang, Kaiming, Zheludev, Ivan N., Moult, John, Kryshtafovych, Andriy

“…The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who…”
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Assessment of three‐dimensional RNA structure prediction in CASP15 by Das, Rhiju, Kretsch, Rachael C., Simpkin, Adam J., Mulvaney, Thomas, Pham, Phillip, Rangan, Ramya, Bu, Fan, Keegan, Ronan M., Topf, Maya, Rigden, Daniel J., Miao, Zhichao, Westhof, Eric

“…The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first…”
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New prediction categories in CASP15 by Kryshtafovych, Andriy, Antczak, Maciej, Szachniuk, Marta, Zok, Tomasz, Kretsch, Rachael C., Rangan, Ramya, Pham, Phillip, Das, Rhiju, Robin, Xavier, Studer, Gabriel, Durairaj, Janani, Eberhardt, Jerome, Sweeney, Aaron, Topf, Maya, Schwede, Torsten, Fidelis, Krzysztof, Moult, John

“…Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments change with the need to address specific problems in structure…”
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Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses by Kretsch, Rachael C, Xu, Lily, Zheludev, Ivan N, Zhou, Xueting, Huang, Rui, Nye, Grace, Li, Shanshan, Zhang, Kaiming, Chiu, Wah, Das, Rhiju

“…Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the…”
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Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome by Zhang, Kaiming, Zheludev, Ivan N., Hagey, Rachel J., Haslecker, Raphael, Hou, Yixuan J., Kretsch, Rachael, Pintilie, Grigore D., Rangan, Ramya, Kladwang, Wipapat, Li, Shanshan, Wu, Marie Teng-Pei, Pham, Edward A., Bernardin-Souibgui, Claire, Baric, Ralph S., Sheahan, Timothy P., D’Souza, Victoria, Glenn, Jeffrey S., Chiu, Wah, Das, Rhiju

“…Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA genome. The highly conserved frameshift stimulation element (FSE),…”
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CASP15 cryo‐EM protein and RNA targets: Refinement and analysis using experimental maps by Mulvaney, Thomas, Kretsch, Rachael C., Elliott, Luc, Beton, Joseph G., Kryshtafovych, Andriy, Rigden, Daniel J., Das, Rhiju, Topf, Maya

“…CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are…”
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De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures by Rangan, Ramya, Watkins, Andrew M, Chacon, Jose, Kretsch, Rachael, Kladwang, Wipapat, Zheludev, Ivan N, Townley, Jill, Rynge, Mats, Thain, Gregory, Das, Rhiju

“…Abstract The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome…”
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Interpretation of RNA cryo-EM maps of various resolutions by Kretsch, Rachael, Das, Rhiju, Chiu, Wah

“…Abstract only…”
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Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package by Mermelstein, Daniel J., Lin, Charles, Nelson, Gard, Kretsch, Rachael, McCammon, J. Andrew, Walker, Ross C.

“…Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of…”
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Cover Image, Volume 91, Issue 12 by Das, Rhiju, Kretsch, Rachael C., Simpkin, Adam J., Mulvaney, Thomas, Pham, Phillip, Rangan, Ramya, Bu, Fan, Keegan, Ronan M., Topf, Maya, Rigden, Daniel J., Miao, Zhichao, Westhof, Eric

“…Reverse Cover: The cover image is based on the Research Article Assessment of three‐dimensional RNA structure prediction in CASP15 by Rhiju Das and Rachael C…”
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Ensemble-function relationships to connect structure to mechanism: application of EnsemblePDB to the serine protease reaction coordinate and its catalytic features by Du, Siyuan, Kretsch, Rachael C., Parres-Gold, Jacob, Peñaherrera, Daniel A., Yabukarski, Filip, Pinney, Margaux M., Herschlag, Dan

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RNA target highlights in CASP15 : Evaluation of predicted models by structure providers by Kretsch, Rachael C., Andersen, Ebbe S., Bujnicki, Janusz M., Chiu, Wah, Das, Rhiju, Luo, Bingnan, Masquida, Benoît, McRae, Ewan K. S., Schroeder, Griffin M., Su, Zhaoming, Wedekind, Joseph E., Xu, Lily, Zhang, Kaiming, Zheludev, Ivan N., Moult, John, Kryshtafovych, Andriy

“…Abstract The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists…”
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