Search Results - "Croll, Tristan"

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement by McCallum, Matthew, Czudnochowski, Nadine, Rosen, Laura E, Zepeda, Samantha K, Bowen, John E, Walls, Alexandra C, Hauser, Kevin, Joshi, Anshu, Stewart, Cameron, Dillen, Josh R, Powell, Abigail E, Croll, Tristan I, Nix, Jay, Virgin, Herbert W, Corti, Davide, Snell, Gyorgy, Veesler, David

“…The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or…”
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UCSF ChimeraX: Structure visualization for researchers, educators, and developers by Pettersen, Eric F., Goddard, Thomas D., Huang, Conrad C., Meng, Elaine C., Couch, Gregory S., Croll, Tristan I., Morris, John H., Ferrin, Thomas E.

“…UCSF ChimeraX is the next‐generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following…”
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Improved AlphaFold modeling with implicit experimental information by Terwilliger, Thomas C., Poon, Billy K., Afonine, Pavel V., Schlicksup, Christopher J., Croll, Tristan I., Millán, Claudia, Richardson, Jane. S., Read, Randy J., Adams, Paul D.

“…Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some…”
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Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV‑2 Spike Protein in a Viral Membrane by Choi, Yeol Kyo, Cao, Yiwei, Frank, Martin, Woo, Hyeonuk, Park, Sang-Jun, Yeom, Min Sun, Croll, Tristan I, Seok, Chaok, Im, Wonpil

“…The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2…”
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Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain by Croll, Tristan I., Smith, Brian J., Margetts, Mai B., Whittaker, Jonathan, Weiss, Michael A., Ward, Colin W., Lawrence, Michael C.

“…Insulin receptor (IR) signaling is critical to controlling nutrient uptake and metabolism. However, only a low-resolution (3.8 Å) structure currently exists…”
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Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE by Oeffner, Robert D., Croll, Tristan I., Millán, Claudia, Poon, Billy K., Schlicksup, Christopher J., Read, Randy J., Terwilliger, Tom C.

“…AlphaFold has recently become an important tool in providing models for experimental structure determination by X‐ray crystallography and cryo‐EM. Large parts…”
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Evaluation of template‐based modeling in CASP13 by Croll, Tristan I., Sammito, Massimo D., Kryshtafovych, Andriy, Read, Randy J.

“…Performance in the template‐based modeling (TBM) category of CASP13 is assessed here, using a variety of metrics. Performance of the predictor groups that…”
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A structural biology community assessment of AlphaFold2 applications by Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M., Davey, Norman E., Stein, Amelie, Elofsson, Arne, Croll, Tristan I., Beltrao, Pedro

“…Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in…”
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AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination by Terwilliger, Thomas C., Liebschner, Dorothee, Croll, Tristan I., Williams, Christopher J., McCoy, Airlie J., Poon, Billy K., Afonine, Pavel V., Oeffner, Robert D., Richardson, Jane S., Read, Randy J., Adams, Paul D.

“…Artificial intelligence-based protein structure prediction methods such as AlphaFold have revolutionized structural biology. The accuracies of these…”
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SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape by Starr, Tyler N., Czudnochowski, Nadine, Liu, Zhuoming, Zatta, Fabrizia, Park, Young-Jun, Addetia, Amin, Pinto, Dora, Beltramello, Martina, Hernandez, Patrick, Greaney, Allison J., Marzi, Roberta, Glass, William G., Zhang, Ivy, Dingens, Adam S., Bowen, John E., Tortorici, M. Alejandra, Walls, Alexandra C., Wojcechowskyj, Jason A., De Marco, Anna, Rosen, Laura E., Zhou, Jiayi, Montiel-Ruiz, Martin, Kaiser, Hannah, Dillen, Josh R., Tucker, Heather, Bassi, Jessica, Silacci-Fregni, Chiara, Housley, Michael P., di Iulio, Julia, Lombardo, Gloria, Agostini, Maria, Sprugasci, Nicole, Culap, Katja, Jaconi, Stefano, Meury, Marcel, Dellota Jr, Exequiel, Abdelnabi, Rana, Foo, Shi-Yan Caroline, Cameroni, Elisabetta, Stumpf, Spencer, Croll, Tristan I., Nix, Jay C., Havenar-Daughton, Colin, Piccoli, Luca, Benigni, Fabio, Neyts, Johan, Telenti, Amalio, Lempp, Florian A., Pizzuto, Matteo S., Chodera, John D., Hebner, Christy M., Virgin, Herbert W., Whelan, Sean P. J., Veesler, David, Corti, Davide, Bloom, Jesse D., Snell, Gyorgy

“…An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape 1 – 3 , have activity against diverse sarbecoviruses 4 – 7 , and be highly protective…”
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Developing a Fully Glycosylated Full-Length SARS-CoV‑2 Spike Protein Model in a Viral Membrane by Woo, Hyeonuk, Park, Sang-Jun, Choi, Yeol Kyo, Park, Taeyong, Tanveer, Maham, Cao, Yiwei, Kern, Nathan R, Lee, Jumin, Yeom, Min Sun, Croll, Tristan I, Seok, Chaok, Im, Wonpil

“…This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First,…”
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Cryo-EM Structure of the Rhodobacter sphaeroides Light-Harvesting 2 Complex at 2.1 Å by Qian, Pu, Swainsbury, David J. K, Croll, Tristan I, Castro-Hartmann, Pablo, Divitini, Giorgio, Sader, Kasim, Hunter, C. Neil

“…Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such…”
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Macromolecular structure determination using X‐rays, neutrons and electrons: recent developments in Phenix by Liebschner, Dorothee, Afonine, Pavel V., Baker, Matthew L., Bunkóczi, Gábor, Chen, Vincent B., Croll, Tristan I., Hintze, Bradley, Hung, Li-Wei, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D., Poon, Billy K., Prisant, Michael G., Read, Randy J., Richardson, Jane S., Richardson, David C., Sammito, Massimo D., Sobolev, Oleg V., Stockwell, Duncan H., Terwilliger, Thomas C., Urzhumtsev, Alexandre G., Videau, Lizbeth L., Williams, Christopher J., Adams, Paul D.

“…Diffraction (X‐ray, neutron and electron) and electron cryo‐microscopy are powerful methods to determine three‐dimensional macromolecular structures, which are…”
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Accelerating crystal structure determination with iterative AlphaFold prediction by Terwilliger, Thomas C., Afonine, Pavel V., Liebschner, Dorothee, Croll, Tristan I., McCoy, Airlie J., Oeffner, Robert D., Williams, Christopher J., Poon, Billy K., Richardson, Jane S., Read, Randy J., Adams, Paul D.

“…Experimental structure determination can be accelerated with artificial intelligence (AI)‐based structure‐prediction methods such as AlphaFold. Here, an…”
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How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor by Xu, Yibin, Kirk, Nicholas S., Venugopal, Hariprasad, Margetts, Mai B., Croll, Tristan I., Sandow, Jarrod J., Webb, Andrew I., Delaine, Carlie A., Forbes, Briony E., Lawrence, Michael C.

“…Human type 1 insulin-like growth factor receptor (IGF-1R) signals chiefly in response to the binding of insulin-like growth factor I. Relatively little is…”
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Structure of CD20 in complex with the therapeutic monoclonal antibody rituximab by Rougé, Lionel, Chiang, Nancy, Steffek, Micah, Kugel, Christine, Croll, Tristan I, Tam, Christine, Estevez, Alberto, Arthur, Christopher P, Koth, Christopher M, Ciferri, Claudio, Kraft, Edward, Payandeh, Jian, Nakamura, Gerald, Koerber, James T, Rohou, Alexis

“…Cluster of differentiation 20 (CD20) is a B cell membrane protein that is targeted by monoclonal antibodies for the treatment of malignancies and autoimmune…”
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Improving SARS-CoV-2 structures: Peer review by early coordinate release by Croll, Tristan I., Williams, Christopher J., Chen, Vincent B., Richardson, David C., Richardson, Jane S.

“…This work builds upon the record-breaking speed and generous immediate release of new experimental three-dimensional structures of the severe acute respiratory…”
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Ligand recognition and G-protein coupling selectivity of cholecystokinin A receptor by Liu, Qiufeng, Yang, Dehua, Zhuang, Youwen, Croll, Tristan I., Cai, Xiaoqing, Dai, Antao, He, Xinheng, Duan, Jia, Yin, Wanchao, Ye, Chenyu, Zhou, Fulai, Wu, Beili, Zhao, Qiang, Xu, H. Eric, Wang, Ming-Wei, Jiang, Yi

“…Cholecystokinin A receptor (CCK A R) belongs to family A G-protein-coupled receptors and regulates nutrient homeostasis upon stimulation by cholecystokinin…”
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Catalytic trajectory of a dimeric nonribosomal peptide synthetase subunit with an inserted epimerase domain by Wang, Jialiang, Li, Dandan, Chen, Lu, Cao, Wei, Kong, Liangliang, Zhang, Wei, Croll, Tristan, Deng, Zixin, Liang, Jingdan, Wang, Zhijun

“…Nonribosomal peptide synthetases (NRPSs) are modular assembly-line megaenzymes that synthesize diverse metabolites with wide-ranging biological activities. The…”
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Multiple functional self-association interfaces in plant TIR domains by Zhang, Xiaoxiao, Bernoux, Maud, Bentham, Adam R., Newman, Toby E., Ve, Thomas, Casey, Lachlan W., Raaymakers, Tom M., Hu, Jian, Croll, Tristan I., Schreiber, Karl J., Staskawicz, Brian J., Anderson, Peter A., Sohn, Kee Hoon, Williams, Simon J., Dodds, Peter N., Kobe, Bostjan

“…The self-association of Toll/interleukin-1 receptor/resistance protein (TIR) domains has been implicated in signaling in plant and animal immunity receptors…”
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