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Time-resolved structural studies with serial crystallography: A new light on retinal proteins

29 Jun 2015 | BioXFEL Publications | Contributor(s): Valérie Panneels, Wenting Wu, Ching-Ju Tsai, Przemek Nogly, Jan Rheinberger, Kathrin Jaeger, Gregor Cicchetti, Cornelius Gati, Leonhard M. Kick, Leonardo Sala, Guido Capitani, Chris Milne, Celestino Padeste, Bill Pedrini, Xiao-Dan Li, Jörg Standfuss, Rafael Abela, Gebhard F.X. Schertler

journal-article http://dx.doi.org/10.1063/1.4922774 NSF-STC Biology with X-ray Lasers (NSF-1231306) Panneels, V. et al., 2015. Time-resolved structural studies with serial crystallography: A new light on retinal proteins. Structural Dynamics, 2(4), p.041718. Available at: …

Toward Analysis of Proteins in Single Cells: A Quantitative Approach Employing Isobaric Tags with MALDI Mass Spectrometry Realized with a Microfluidic Platform

03 Jun 2016 | BioXFEL Publications | Contributor(s): Mian Yang, Randall Nelson, Alexandra Ros

http://dx.doi.org/10.1021/acs.analchem.5b03419 journal-article Yang, M., Nelson, R. & Ros, A., 2016. Toward Analysis of Proteins in Single Cells: A Quantitative Approach Employing Isobaric Tags with MALDI Mass Spectrometry Realized with a Microfluidic Platform. Analytical Chemistry, 88(13), …

Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers

15 Aug 2014 | BioXFEL Publications | Contributor(s): S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, A. Barty, C. Bostedt, J. Bozek, R. Coffee, S. Epp, B. Erk, L. Foucar, R. Hartmann, N. Kimmel, K-U. Kühnel, J. Maurer, M. Messerschmidt, B. Rudek, D. Starodub, J. Thøgersen, G. Weidenspointner, T. A. White, H. Stapelfeldt, D. Rolles, H. N. Chapman, J. Küpper

http://dx.doi.org/10.1039/c4fd00028e S. Stern and L. Holmegaard and F. Filsinger and A. Rouzée and A. Rudenko and P. Johnsson and A. V. Martin and A. Barty and C. Bostedt and J. Bozek and R. Coffee and S. Epp and B. Erk and L. Foucar and R. Hartmann and N. Kimmel and K-U. Kühnel and J. Maurer and …

Toward G protein-coupled receptor structure-based drug design using X-ray lasers

24 Oct 2019 | BioXFEL Publications | Contributor(s): Andrii Ishchenko, Benjamin Stauch, Gye Won Han, Alexander Batyuk, Anna Shiriaeva, Chufeng Li, Nadia Zatsepin, Uwe Weierstall, Wei Liu, Eriko Nango, Takanori Nakane, Rie Tanaka, Kensuke Tono, Yasumasa Joti, So Iwata, Isabel Moraes, Cornelius Gati, Vadim Cherezov

http://dx.doi.org/10.1107/s2052252519013137 Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. …

Toward steering a jet of particles into an x-ray beam with optically induced forces

25 Aug 2015 | BioXFEL Publications | Contributor(s): Niko Eckerskorn, Richard Bowman, Richard Kirian, Salah Awel, Max Oliver Wiedorn, Jochen Küpper, Miles J. Padgett, Henry Chapman, Andrei V. Rode

http://dx.doi.org/10.1117/12.2191442 Niko Eckerskorn and Richard Bowman and Richard A. Kirian and Salah Awel and Max Wiedorn and Jochen Küpper and Miles J. Padgett and Henry N. Chapman and Andrei V. Rode Eckerskorn, N. et al., 2015. Toward steering a jet of particles into an x-ray beam with …

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers

14 Nov 2013 | BioXFEL Publications | Contributor(s): Hyung Joo Park, N. Duane Loh, Raymond G. Sierra, Christina Y. Hampton, Dmitri Starodub, Andrew V. Martin, Anton Barty, Andrew Aquila, Joachim Schulz, Jan Steinbrener, Robert L. Shoeman, Lukas Lomb, Stephan Kassemeyer, Christoph Bostedt, John Bozek, Sascha W. Epp, Benjamin Erk, Robert Hartmann, Daniel Rolles, Artem Rudenko, Benedikt Rudek, Lutz Foucar, Nils Kimmel, Georg Weidenspointner, Guenter Hauser, Peter Holl, Emanuele Pedersoli, Mengning Liang, Mark S. Hunter, Lars Gumprecht, Nicola Coppola, Cornelia Wunderer, Heinz Graafsma, Filipe R.N.C. Maia, Tomas Ekeberg, Max Hantke, Holger Fleckenstein, Helmut Hirsemann, Karol Nass, Herbert J. Tobias, George R. Farquar, W. Henry Benner, Stefan Hau-Riege, Christian Reich, Andreas Hartmann, Heike Soltau, Stefano Marchesini, Sasa Bajt, Miriam Barthelmess, Lothar Strueder, Joachim Ullrich, Philip Bucksbaum, Matthias Frank, Ilme Schlichting, Henry Chapman, Michael J. Bogan, Veit Elser

journal-article http://dx.doi.org/10.1364/oe.21.028729 Park, H.J. et al., 2013. Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers. Optics Express, 21(23), p.28729. Available at: http://dx.doi.org/10.1364/oe.21.028729. Hyung Joo Park …

Towards a generalised approach for the time-resolved crystallographic study of enzymes

05 Jan 2016 | BioXFEL Publications | Contributor(s): Diana C. F. Monteiro, Vijay Patel, Christopher P. Bartlett, Shingo Nozaki, Thomas D. Grant, James A. Gowdy, Gary S. Thompson, Arnout P. Kalverda, Edward Snell, Hironori Niki, Arwen R. Pearson, Michael E. Webb

http://dx.doi.org/10.1107/s205327331509957x Diana C. F. Monteiro and Vijay Patel and Christopher P. Bartlett and Shingo Nozaki and Thomas D. Grant and James A. Gowdy and Gary S. Thompson and Arnout P. Kalverda and Edward H. Snell and Hironori Niki and Arwen R. Pearson and Michael E. Webb Monteiro, …

Towards phasing using high X-ray intensity

29 Sep 2015 | BioXFEL Publications | Contributor(s): Lorenzo Galli, Sang-Kil Son, Thomas R. M. Barends, Thomas A. White, Anton Barty, Sabine Botha, Sébastien Boutet, Carl Caleman, R. Bruce Doak, Max H. Nanao, Karol Nass, Robert L. Shoeman, Nicusor Timneanu, Robin Santra, Ilme Schlichting, Henry Chapman

X-ray free-electron lasers (XFELs) show great promise for macromolecular structure determination from sub-micrometre-sized crystals, using the emerging method of serial femtosecond crystallography. The extreme brightness of the XFEL radiation can multiply ionize most, if not all, atoms in a …

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

18 Apr 2013 | BioXFEL Publications | Contributor(s): David J. Kissick, Christopher M. Dettmar, Michael Becker, Anne M. Mulichak, Vadim Cherezov, Stephan L. Ginell, Kevin P. Battaile, Lisa J. Keefe, Robert F. Fischetti, Garth J. Simpson

http://dx.doi.org/10.1107/s0907444913002746 journal-article Kissick, D.J. et al., 2013. Towards protein-crystal centering using second-harmonic generation (SHG) microscopy. Acta Crystallographica Section D Biological Crystallography, 69(5), pp.843–851. Available at: …

Towards RIP using free-electron laser SFX data

04 Feb 2015 | BioXFEL Publications | Contributor(s): Lorenzo Galli, Sang-Kil Son, Thomas A. White, Robin Santra, Henry Chapman, Max H. Nanao

Here, it is shown that simulated native serial femtosecond crystallography (SFX) cathepsin B data can be phased by rapid ionization of sulfur atoms. Utilizing standard software adopted for radiation-damage-induced phasing (RIP), the effects on both substructure determination and phasing of the …

Towards time-resolved serial crystallography in a microfluidic device

26 Jun 2015 | BioXFEL Publications | Contributor(s): Ashtamurthy S. Pawate, Vukica Šrajer, Jeremy Schieferstein, Sudipto Guha, Robert Henning, Irina Kosheleva, Marius Schmidt, Zhong Ren, Paul J. A. Kenis, Sarah Perry

Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction …

Toxicity of Eosinophil MBP Is Repressed by Intracellular Crystallization and Promoted by Extracellular Aggregation

26 Feb 2015 | BioXFEL Publications | Contributor(s): Alice Soragni, Shida Yousefi, Christina Stoeckle, Angela B. Soriaga, Michael R. Sawaya, Evelyne Kozlowski, Inès Schmid, Susanne Radonjic-Hoesli, Sebastien Boutet, Garth J. Williams, Marc Messerschmidt, M. Marvin Seibert, Duilio Cascio, Nadia A. Zatsepin, Manfred Burghammer, Christian Riekel, Jacques-Philippe Colletier, Roland Riek, David S. Eisenberg, Hans-Uwe Simon

http://dx.doi.org/10.1016/j.molcel.2015.01.026 Alice Soragni and Shida Yousefi and Christina Stoeckle and Angela B. Soriaga and Michael R. Sawaya and Evelyne Kozlowski and Inès Schmid and Susanne Radonjic-Hoesli and Sebastien Boutet and Garth J. Williams and Marc Messerschmidt and M. Marvin …

Trace phase detection and strain characterization from serial X-ray free-electron laser crystallography of a Pr0.5Ca0.5MnO3 powder

17 Nov 2014 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, Christian Jooss, Anton Barty, Richard Bean, Sébastien Boutet, Sarnjeet S. Dhesi, R. Bruce Doak, Michael Först, Lorenzo Galli, Richard Kirian, Joseph Kozak, Michael Lang, Roman Mankowsky, Marc Messerschmidt, John Spence, Dingjie Wang, Uwe Weierstall, Thomas A. White, Garth J. Williams, Oleksandr Yefanov, Nadia Zatsepin, Andrea Cavalleri, Henry Chapman

http://dx.doi.org/10.1017/s0885715614001171 We report on the analysis of virtual powder-diffraction patterns from serial femtosecond crystallography (SFX) data collected at an X-ray free-electron laser. Different approaches to binning and normalizing these patterns are discussed with respect to the …

Trajectories of the ribosome as a Brownian nanomachine

24 Nov 2014 | BioXFEL Publications | Contributor(s): Ali Dashti, Peter Schwander, Robert Langlois, Russell Fung, Wen Li, Ahmad Hosseinizadeh, Hstau Y. Liao, Jesper Pallesen, Gyanesh Sharma, Vera A. Stupina, Anne E. Simon, Jonathan D. Dinman, Joachim Frank, Abbas Ourmazd

http://dx.doi.org/10.1073/pnas.1419276111 Ali Dashti and Peter Schwander and Robert Langlois and Russell Fung and Wen Li and Ahmad Hosseinizadeh and Hstau Y. Liao and Jesper Pallesen and Gyanesh Sharma and Vera A. Stupina and Anne E. Simon and Jonathan D. Dinman and Joachim Frank and Abbas Ourmazd …

Trajectories of the ribosome as a Brownian nanomachine

12 Apr 2018 | BioXFEL Publications | Contributor(s): Ali Dashti, Peter Schwander, Robert Langlois, Russell Fung, Wen Li, Ahmad Hosseinizadeh, Hstau Y. Liao, Jesper Pallesen, Gyanesh Sharma, Vera A. Stupina, Anne E. Simon, Jonathan D. Dinman, Joachim Frank, Abbas Ourmazd

http://dx.doi.org/10.1142/9789813234864_0048 book-chapter Dashti, A. et al., 2018. Trajectories of the ribosome as a Brownian nanomachine. Single-Particle Cryo-Electron Microscopy, pp.463–475. Available at: http://dx.doi.org/10.1142/9789813234864_0048. Ali Dashti and Peter Schwander and Robert …

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms

14 Apr 2014 | BioXFEL Publications | Contributor(s): V. Schweikhard, C. Meng, K. Murakami, C. D. Kaplan, R. D. Kornberg, S. M. Block

journal-article http://dx.doi.org/10.1073/pnas.1405181111 Schweikhard, V. et al., 2014. Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms. Proceedings of the National Academy of Sciences, 111(18), pp.6642–6647. …

Transferring the entatic-state principle to copper photochemistry

15 Jan 2018 | BioXFEL Publications | Contributor(s): B. Dicke, A. Hoffmann, J. Stanek, M. S. Rampp, B. Grimm-Lebsanft, F. Biebl, D. Rukser, B. Maerz, D. Göries, M. Naumova, M. Biednov, G. Neuber, A. Wetzel, S. M. Hofmann, P. Roedig, A. Meents, J. Bielecki, J. Andreasson, K. R. Beyerlein, H. N. Chapman, C. Bressler, W. Zinth, M. Rübhausen, S. Herres-Pawlis

http://dx.doi.org/10.1038/nchem.2916 journal-article Dicke, B. et al., 2018. Transferring the entatic-state principle to copper photochemistry. Nature Chemistry. Available at: http://dx.doi.org/10.1038/nchem.2916. B. Dicke and A. Hoffmann and J. Stanek and M. S. Rampp and B. Grimm-Lebsanft and …

Transient lattice contraction in the solid-to-plasma transition

29 Jan 2016 | BioXFEL Publications | Contributor(s): Ken R. Ferguson, Maximilian Bucher, Tais Gorkhover, Sébastien Boutet, Hironobu Fukuzawa, Jason E. Koglin, Yoshiaki Kumagai, Alberto Lutman, Agostino Marinelli, Marc Messerschmidt, Kiyonobu Nagaya, Jim Turner, Kiyoshi Ueda, Garth J. Williams, Philip H. Bucksbaum, Christoph Bostedt

http://dx.doi.org/10.1126/sciadv.1500837 Ken R. Ferguson and Maximilian Bucher and Tais Gorkhover and Sébastien Boutet and Hironobu Fukuzawa and Jason E. Koglin and Yoshiaki Kumagai and Alberto Lutman and Agostino Marinelli and Marc Messerschmidt and Kiyonobu Nagaya and Jim Turner and Kiyoshi Ueda …

Transient state measurements on proteins by time-resolved crystallography

22 Apr 2022 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Marius Schmidt

http://dx.doi.org/10.1016/j.sbi.2022.102376 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Malla, T. N., & Schmidt, M. (2022). Transient state measurements on proteins by time-resolved crystallography. Current Opinion in Structural Biology, 74, 102376. …

Transmission electron microscopy for the evaluation and optimization of crystal growth

26 Apr 2016 | BioXFEL Publications | Contributor(s): Hilary P. Stevenson, Guowu Lin, Christopher Barnes, Ieva Sutkeviciute, Troy Krzysiak, Simon C. Weiss, Shelley Reynolds, Ying Wu, Veeranagu Nagarajan, Alexander M. Makhov, Robert M Lawrence, Emily Lamm, Lisa Clark, Timothy J. Gardella, Brenda Hogue, Craig M. Ogata, Jinwoo Ahn, Angela M. Gronenborn, James F. Conway, Jean-Pierre Vilardaga, Aina E. Cohen, Guillermo Calero

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that …

Tuning RNA Flexibility with Helix Length and Junction Sequence

15 Dec 2015 | BioXFEL Publications | Contributor(s): Julie L. Sutton, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2015.10.039 journal-article Sutton, J.L. & Pollack, L., 2015. Tuning RNA Flexibility with Helix Length and Junction Sequence. Biophysical Journal, 109(12), pp.2644–2653. Available at: http://dx.doi.org/10.1016/j.bpj.2015.10.039. Julie L. Sutton and Lois Pollack

Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray scattering experiments

21 Oct 2021 | BioXFEL Publications | Contributor(s): Michael Thompson, Alexander Wolff, Benjamin Barad, Wilson Nieves Vasquez, Nathaniel Brown, Hyun Sun Cho, Friedrich Schotte, Valentyn Stadnytskyi, Philip Anfinrud, James Fraser

http://dx.doi.org/10.1107/s0108767321097841 journal-article Thompson, M., Wolff, A., Barad, B., Vasquez, W. N., Brown, N., Cho, H. S., Schotte, F., Stadnytskyi, V., Anfinrud, P., & Fraser, J. (2021). Turning up the heat on molecular machines with multi-temperature and temperature-jump X-ray …

Two disparate ligand-binding sites in the human P2Y1 receptor

30 Mar 2015 | BioXFEL Publications | Contributor(s): Dandan Zhang, Zhan-Guo Gao, Kaihua Zhang, Evgeny Kiselev, Steven Crane, Jiang Wang, Silvia Paoletta, Cuiying Yi, Limin Ma, Wenru Zhang, Gye Won Han, Hong Liu, Vadim Cherezov, Vsevolod Katritch, Hualiang Jiang, Raymond C. Stevens, Kenneth A. Jacobson, Qiang Zhao, Beili Wu

http://dx.doi.org/10.1038/nature14287 Dandan Zhang and Zhan-Guo Gao and Kaihua Zhang and Evgeny Kiselev and Steven Crane and Jiang Wang and Silvia Paoletta and Cuiying Yi and Limin Ma and Wenru Zhang and Gye Won Han and Hong Liu and Vadim Cherezov and Vsevolod Katritch and Hualiang Jiang and …

Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser

12 Feb 2021 | BioXFEL Publications | Contributor(s): Thomas D. Grant, Suchithranga M.D.C. Perera, Leslie A. Salas-Estrada, Andrey V. Struts, Udeep Chawla, Steven D.E. Fried, Nipuna Weerasinghe, Kostantinos Karpos, Domingo Meza, Nadia Zatsepin, Alan Grossfield, Derek Mendez, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2020.11.1006 journal-article Grant, T.D. et al., 2021. Ultrafast Membrane Protein Dynamics Revealed by X-Ray Scattering with a Femtosecond Free-Electron Laser. Biophysical Journal, 120(3), p.133a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1006. Thomas …

Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser

14 May 2018 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, H. Olof Jönsson, Roberto Alonso-Mori, Andrew Aquila, Saša Bajt, Anton Barty, Richard Bean, Jason E. Koglin, Marc Messerschmidt, Davide Ragazzon, Dimosthenis Sokaras, Garth J. Williams, Stefan Hau-Riege, Sébastien Boutet, Henry Chapman, Nicuşor Tîmneanu, Carl Caleman

http://dx.doi.org/10.1073/pnas.1711220115 journal-article Beyerlein, K.R. et al., 2018. Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser. Proceedings of the National Academy of Sciences, p.201711220. Available at: http://dx.doi.org/10.1073/pnas.1711220115. Kenneth …

Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser

20 Jan 2015 | BioXFEL Publications | Contributor(s): Carl Caleman, Nicuşor Tîmneanu, Andrew V. Martin, H. Olof Jönsson, Andrew Aquila, Anton Barty, Howard A. Scott, Thomas A. White, Henry Chapman

http://dx.doi.org/10.1364/oe.23.001213 Carl Caleman and Nicuşor Tîmneanu and Andrew V. Martin and H. Olof Jönsson and Andrew Aquila and Anton Barty and Howard A. Scott and Thomas A. White and Henry N. Chapman Caleman, C. et al., 2015. Ultrafast self-gating Bragg diffraction of exploding …

Ultrafast Three-Dimensional Imaging of Lattice Dynamics in Individual Gold Nanocrystals

24 May 2013 | BioXFEL Publications | Contributor(s): J. N. Clark, L. Beitra, G. Xiong, A. Higginbotham, D. M. Fritz, H. T. Lemke, D. Zhu, M. Chollet, G. J. Williams, M. Messerschmidt, B. Abbey, R. J. Harder, A. M. Korsunsky, J. S. Wark, I. K. Robinson

http://dx.doi.org/10.1126/science.1236034 journal-article Clark, J.N. et al., 2013. Ultrafast Three-Dimensional Imaging of Lattice Dynamics in Individual Gold Nanocrystals. Science, 341(6141), pp.56–59. Available at: http://dx.doi.org/10.1126/science.1236034. J. N. Clark and L. Beitra and G. …

Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature

17 Jun 2014 | BioXFEL Publications | Contributor(s): J. A. Sellberg, C. Huang, T. A. McQueen, N. D. Loh, H. Laksmono, D. Schlesinger, R. G. Sierra, D. Nordlund, C. Y. Hampton, D. Starodub, D. P. DePonte, M. Beye, C. Chen, A. V. Martin, A. Barty, K. T. Wikfeldt, T. M. Weiss, C. Caronna, J. Feldkamp, L. B. Skinner, M. M. Seibert, M. Messerschmidt, G. J. Williams, S. Boutet, L. G. M. Pettersson, M. J. Bogan, A. Nilsson

journal-article http://dx.doi.org/10.1038/nature13266 Sellberg, J.A. et al., 2014. Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature. Nature, 510(7505), pp.381–384. Available at: http://dx.doi.org/10.1038/nature13266. J. A. Sellberg and C. Huang and T. …

Uncoupling Promoter Opening from Start-Site Scanning

13 Jun 2015 | BioXFEL Publications | Contributor(s): Kenji Murakami, Pierre-Jean Mattei, Ralph E. Davis, Huiyan Jin, Craig D. Kaplan, Roger D. Kornberg

journal-article http://dx.doi.org/10.1016/j.molcel.2015.05.021 Murakami, K. et al., 2015. Uncoupling Promoter Opening from Start-Site Scanning. Molecular Cell, 59(1), pp.133–138. Available at: http://dx.doi.org/10.1016/j.molcel.2015.05.021. Kenji Murakami and Pierre-Jean Mattei and Ralph E. …

Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT fromSulfolobus solfataricus

20 Mar 2014 | BioXFEL Publications | Contributor(s): Fengbin Wang, Shanteri Singh, Jianjun Zhang, Tyler D. Huber, Kate E. Helmich, Manjula Sunkara, Katherine A. Hurley, Randal D. Goff, Craig A. Bingman, Andrew J. Morris, Jon S. Thorson, George Phillips

http://dx.doi.org/10.1111/febs.12784 journal-article Wang, F. et al., 2014. Understanding molecular recognition of promiscuity of thermophilic methionine adenosyltransferase sMAT fromSulfolobus solfataricus. FEBS Journal, 281(18), pp.4224–4239. Available at: …

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

25 May 2016 | BioXFEL Publications | Contributor(s): Suzette A. Pabit, Andrea Katz, Igor S. Tolokh, Aleksander Drozdetski, Nathan Baker, Alexey V. Onufriev, Lois Pollack

http://dx.doi.org/10.1063/1.4950814 journal-article Pabit, S.A. et al., 2016. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations. The Journal of Chemical Physics, 144(20), p.205102. Available at: …

Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus)

25 Mar 2015 | BioXFEL Publications | Contributor(s): Lindsay L Traeger, Jeremy D Volkening, Howell Moffett, Jason R Gallant, Po-Hao Chen, Carl D Novina, George Phillips, Rene Anand, Gregg B Wells, Matthew Pinch, Robert Güth, Graciela A Unguez, James S Albert, Harold Zakon, Michael R Sussman, Manoj P Samanta

http://dx.doi.org/10.1186/s12864-015-1288-8 Lindsay L Traeger and Jeremy D Volkening and Howell Moffett and Jason R Gallant and Po-Hao Chen and Carl D Novina and George N Phillips and Rene Anand and Gregg B Wells and Matthew Pinch and Robert Güth and Graciela A Unguez and James S Albert and Harold …

Use of transmission electron microscopy to identify nanocrystals of challenging protein targets

28 May 2014 | BioXFEL Publications | Contributor(s): H. P. Stevenson, A. M. Makhov, M. Calero, A. L. Edwards, O. B. Zeldin, I. I. Mathews, G. Lin, C. O. Barnes, H. Santamaria, T. M. Ross, S. M. Soltis, C. Khosla, V. Nagarajan, J. F. Conway, A. E. Cohen, G. Calero

http://dx.doi.org/10.1073/pnas.1400240111 journal-article Stevenson, H.P. et al., 2014. Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proceedings of the National Academy of Sciences, 111(23), pp.8470–8475. Available at: …

Use of triple correlations for the sign determinations of expansion coefficients of symmetric approximations to the diffraction volumes of regular viruses

18 Jun 2015 | BioXFEL Publications | Contributor(s): H. C. Poon, D. K. Saldin

http://dx.doi.org/10.1063/1.4922476 H. C. Poon and D. K. Saldin Poon, H.C. & Saldin, D.K., 2015. Use of triple correlations for the sign determinations of expansion coefficients of symmetric approximations to the diffraction volumes of regular viruses. Structural Dynamics, 2(4), p.041716. Available …

Using a commodity high-definition television for collaborative structural biology

28 May 2014 | BioXFEL Publications | Contributor(s): Ragothaman Yennamalli, Raj Arangarasan, Aaron Bryden, Michael Gleicher, George Phillips

Visualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure–function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics …

Using deep mutational scanning to identify the determinants of antibiotic resistance

11 Feb 2022 | BioXFEL Publications | Contributor(s): Christian B. Macdonald, Alexis Kelley, Jenna Pellegrino, Willow Coyote-Maestas, James Fraser

http://dx.doi.org/10.1016/j.bpj.2021.11.665 journal-article Macdonald, C. B., Kelley, A., Pellegrino, J., Coyote-Maestas, W., & Fraser, J. (2022). Using deep mutational scanning to identify the determinants of antibiotic resistance. Biophysical Journal, 121(3), 422a. …

Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth

24 Mar 2020 | BioXFEL Publications | Contributor(s): Russell Fung, Jose Villar, Ali Dashti, Leila Cheikh Ismail, Eleonora Staines-Urias, Eric O. Ohuma, Laurent J. Salomon, Cesar G. Victora, Fernando C. Barros, Ann Lambert, Maria Carvalho, Yasmin A. Jaffer, Alison J. Noble, Michael G. Gravett, Manorama Purwar, Ruyan Pang, Enrico Bertino, Shama Munim, Aung Myat Min, Rose McGready, Shane A. Norris, Zulfiqar A Bhutta, Stephen H. Kennedy, Aris T. Papageorghiou, Abbas Ourmazd, International Fetal And Newborn Gro Group

http://dx.doi.org/10.2139/ssrn.3471997 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Fung, R. et al., 2019. Using Machine Learning to Achieve Accurate Estimates of Fetal Gestational Age and Personalized Predictions of Fetal Growth. SSRN Electronic Journal. Available at: …

Using X-ray Diffraction Techniques for Biomimetic Drug Development, Formulation, and Polymorphic Characterization

30 Dec 2020 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Ritika Gautam, Arthur Tinoco

http://dx.doi.org/10.3390/biomimetics6010001 Drug development is a decades-long, multibillion dollar investment that often limits itself. To decrease the time to drug approval, efforts are focused on drug targets and drug formulation for optimal biocompatibility and efficacy. X-ray structural …

Using XFELs to measure the solution structures of biomolecules

13 Oct 2015 | Teaching Materials

Dr. Lois Pollack presents an introduction to small and wide angle X-ray solution scattering techniques and describes the advances made possible by XFELs.

Valence electron energy-loss spectroscopy study of ZrSiO4 and ZrO2

16 Jul 2013 | BioXFEL Publications | Contributor(s): Nan Jiang, John Spence

journal-article http://dx.doi.org/10.1016/j.ultramic.2013.06.021 Jiang, N. & Spence, J.C.H., 2013. Valence electron energy-loss spectroscopy study of ZrSiO4 and ZrO2. Ultramicroscopy, 134, pp.68–76. Available at: http://dx.doi.org/10.1016/j.ultramic.2013.06.021. Nan Jiang and John C.H. Spence

Vibrational Excitations and Low-Energy Electronic Structure of Epoxide-Decorated Graphene

17 Dec 2013 | BioXFEL Publications | Contributor(s): E. C. Mattson, J. E. Johns, K. Pande, R. A. Bosch, S. Cui, M. Gajdardziska-Josifovska, M. Weinert, J. H. Chen, M. C. Hersam, C. J. Hirschmugl

journal-article http://dx.doi.org/10.1021/jz4025386 Mattson, E.C. et al., 2014. Vibrational Excitations and Low-Energy Electronic Structure of Epoxide-Decorated Graphene. The Journal of Physical Chemistry Letters, 5(1), pp.212–219. Available at: http://dx.doi.org/10.1021/jz4025386. E. C. …

Viral RNA Folding Studied through Contrast Variation Small Angle- X Ray Scattering

07 Feb 2020 | BioXFEL Publications | Contributor(s): Josue San Emeterio, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2019.11.1319 journal-article Emeterio, J. S., & Pollack, L. (2020). Viral RNA Folding Studied through Contrast Variation Small Angle- X Ray Scattering. Biophysical Journal, 118(3), 222a. https://doi.org/10.1016/j.bpj.2019.11.1319 Josue San Emeterio and Lois Pollack

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

10 Feb 2020 | BioXFEL Publications | Contributor(s): Reed M. Stein, Hye Jin Kang, John D. McCorvy, Grant C. Glatfelter, Anthony J. Jones, Tao Che, Samuel Slocum, Xi-Ping Huang, Olena Savych, Yurii S. Moroz, Benjamin Stauch, Linda C. Johansson, Vadim Cherezov, Terry Kenakin, John J. Irwin, Brian K. Shoichet, Bryan L. Roth, Margarita L. Dubocovich

http://dx.doi.org/10.1038/s41586-020-2027-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Stein, R.M. et al., 2020. Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. Nature. Available at: http://dx.doi.org/10.1038/s41586-020-2027-0. Reed M. Stein and …

Virus Crystallography

14 Oct 2015 | Teaching Materials | Contributor(s): Robert M Lawrence

Dr. Rob Lawrence describes the unique problems associated with crystallization of virus particles and different methods to overcome them.

Virus Dynamics Studied by Time-Resolved Small Angle X-Ray Scattering

15 Feb 2019 | BioXFEL Publications | Contributor(s): Josue San Emeterio, Lois Pollack

http://dx.doi.org/10.1016/j.bpj.2018.11.2321 journal-article San Emeterio, J., & Pollack, L. (2019). Virus Dynamics Studied by Time-Resolved Small Angle X-Ray Scattering. Biophysical Journal, 116(3), 431a. https://doi.org/10.1016/j.bpj.2018.11.2321 Josue San Emeterio and Lois Pollack

Visualization of biomolecular structures by WAXS and MD

21 Oct 2021 | BioXFEL Publications | Contributor(s): Weiwei He, Yen-Lin Chen, Serdal Kirmizialtin, Lois Pollack

http://dx.doi.org/10.1107/s0108767321098755 journal-article He, W., Chen, Y.-L., Kirmizialtin, S., & Pollack, L. (2021). Visualization of biomolecular structures by WAXS and MD. Acta Crystallographica Section A Foundations and Advances, 77(a1), a124–a124. …

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

13 Oct 2015 | Teaching Materials

We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast …

Visualizing aerosol-particle injection for diffractive-imaging experiments

16 Mar 2016 | BioXFEL Publications | Contributor(s): Salah Awel, Richard Kirian, Niko Eckerskorn, Max Oliver Wiedorn, Daniel A. Horke, Andrei V. Rode, Jochen Küpper, Henry Chapman

http://dx.doi.org/10.1364/oe.24.006507 Salah Awel and Richard A. Kirian and Niko Eckerskorn and Max Wiedorn and Daniel A. Horke and Andrei V. Rode and Jochen Küpper and Henry N. Chapman Awel, S. et al., 2016. Visualizing aerosol-particle injection for diffractive-imaging experiments. Optics …

Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics

05 Dec 2019 | BioXFEL Publications | Contributor(s): Alex Plumridge, Kurt Andresen, Lois Pollack

http://dx.doi.org/10.1021/jacs.9b04461 journal-article Plumridge, A., Andresen, K. & Pollack, L., 2019. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. Journal of the American Chemical Society. Available at: http://dx.doi.org/10.1021/jacs.9b04461. …

Visualizing single-stranded nucleic acids in solution

13 Dec 2016 | BioXFEL Publications | Contributor(s): Alex Plumridge, Steve P. Meisburger, Lois Pollack

http://dx.doi.org/10.1093/nar/gkw1297 journal-article Plumridge, A., Meisburger, S.P. & Pollack, L., 2016. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Research, p.gkw1297. Available at: http://dx.doi.org/10.1093/nar/gkw1297. Alex Plumridge and Steve P. Meisburger and …

Vitamin C Binds to SARS Coronavirus-2 Main Protease Essential for Viral Replication

04 May 2021 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Suraj Pandey, Luis Aldama, Dennisse Feliz, Moraima Noda, Ishwor Poudyal, George Phillips, Emina Stojkovic, Marius Schmidt

http://dx.doi.org/10.1101/2021.05.02.442358 AbstractThere is an urgent need for anti-viral agents that treat and/or prevent Covid-19 caused by SARS-Coronavirus (CoV-2) infections. The replication of the SARS CoV-2 is dependent on the activity of two cysteine proteases, a papain-like protease, …

Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

01 Feb 2013 | BioXFEL Publications | Contributor(s): Yang Ouk Jung, Jae Hyuk Lee, Joonghan Kim, Marius Schmidt, Keith Moffat, Vukica Šrajer, Hyotcherl Ihee

http://dx.doi.org/10.1038/nchem.1565 journal-article Jung, Y.O. et al., 2013. Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nature Chemistry, 5(3), pp.212–220. Available at: …

Watching proteins function with time-resolved x-ray crystallography

03 Jul 2017 | BioXFEL Publications | Contributor(s): Vukica Šrajer, Marius Schmidt

http://dx.doi.org/10.1088/1361-6463/aa7d32 journal-article Šrajer, V. & Schmidt, M., 2017. Watching proteins function with time-resolved x-ray crystallography. Journal of Physics D: Applied Physics, 50(37), p.373001. Available at: http://dx.doi.org/10.1088/1361-6463/aa7d32. Vukica Šrajer and …

What is the outcome of your crystallization experiment

14 Oct 2015 | Teaching Materials | Contributor(s): Joseph Luft

Joe Luft discusses the detection of hits in crystallization screening experiments for both macro and nanocrystals.

What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective

21 Oct 2021 | BioXFEL Publications | Contributor(s): Kara Zielinski, Lois Pollack

http://dx.doi.org/10.1107/s0108767321099219 journal-article Zielinski, K., & Pollack, L. (2021). What it takes for a successful mix-and-inject serial crystallography experiment: from a sample preparation and sample delivery perspective. Acta Crystallographica Section A Foundations and Advances, …

When Your Crystals Bite

14 Oct 2015 | Teaching Materials | Contributor(s): George Phillips

Dr. George Phillips describes properties of crystals such as twinning and other defects and how they can adversely affect crystallographic analysis.

Winning the Battle of Signal vs. Noise

29 Aug 2014 | Teaching Materials

James Holton (UCSF/LBNL) I will review the major sources of error that contribute to macromolecular crystallography (MX) data with a particular focus on MX data from X-ray Free Electron Lasers. The absolute limits will be defined, and the potential of new and future technologies for overcoming …

WNT5A Inhibits Hepatocyte Proliferation and Concludes β-Catenin Signaling in Liver Regeneration

19 Jun 2015 | BioXFEL Publications | Contributor(s): Jing Yang, Antonella Cusimano, Jappmann K. Monga, Morgan E. Preziosi, Filippo Pullara, Guillermo Calero, Richard Lang, Terry P. Yamaguchi, Kari N. Nejak-Bowen, Satdarshan P. Monga

journal-article http://dx.doi.org/10.1016/j.ajpath.2015.04.021 Yang, J. et al., 2015. WNT5A Inhibits Hepatocyte Proliferation and Concludes β-Catenin Signaling in Liver Regeneration. The American Journal of Pathology, 185(8), pp.2194–2205. Available at: …

workspace

17 Oct 2013 | Tools

workspace

X-ray and UV radiation-damage-induced phasing using synchrotron serial crystallography

06 Apr 2018 | BioXFEL Publications | Contributor(s): Nicolas Foos, Carolin Seuring, Robin Schubert, Anja Burkhardt, Olof Svensson, Alke Meents, Henry Chapman, Max H. Nanao

http://dx.doi.org/10.1107/s2059798318001535 Specific radiation damage can be used to determine phases de novo from macromolecular crystals. This method is known as radiation-damage-induced phasing (RIP). One limitation of the method is that the dose of individual data sets must be minimized, which …

X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1s/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7. Available at: http://dx.doi.org/10.2210/pdb4e1s/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. Noinaj …

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis

12 Jun 2012 | BioXFEL Publications | Contributor(s): J.W. Fairman, N. Dautin, D. Wojtowicz, L. Wei, N. Noinaj, T.J. Barnard, E. Udho, A. Finkelstein, T.M. Przytycka, V. Cherezov, S.K. Buchanan

http://dx.doi.org/10.2210/pdb4e1t/pdb component Fairman, J.W. et al., 2012. X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis. Available at: http://dx.doi.org/10.2210/pdb4e1t/pdb. J.W. Fairman and N. Dautin and D. Wojtowicz and L. Wei and N. …

X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

05 Mar 2014 | BioXFEL Publications | Contributor(s): Jochen Küpper, Stephan Stern, Lotte Holmegaard, Frank Filsinger, Arnaud Rouzée, Artem Rudenko, Per Johnsson, Andrew V. Martin, Marcus Adolph, Andrew Aquila, Saša Bajt, Anton Barty, Christoph Bostedt, John Bozek, Carl Caleman, Ryan Coffee, Nicola Coppola, Tjark Delmas, Sascha Epp, Benjamin Erk, Lutz Foucar, Tais Gorkhover, Lars Gumprecht, Andreas Hartmann, Robert Hartmann, Günter Hauser, Peter Holl, Andre Hömke, Nils Kimmel, Faton Krasniqi, Kai-Uwe Kühnel, Jochen Maurer, Marc Messerschmidt, Robert Moshammer, Christian Reich, Benedikt Rudek, Robin Santra, Ilme Schlichting, Carlo Schmidt, Sebastian Schorb, Joachim Schulz, Heike Soltau, John Spence, Dmitri Starodub, Lothar Strüder, Jan Thøgersen, Marc J. J. Vrakking, Georg Weidenspointner, Thomas A. White, Cornelia Wunderer, Gerard Meijer, Joachim Ullrich, Henrik Stapelfeldt, Daniel Rolles, Henry Chapman

http://dx.doi.org/10.1103/physrevlett.112.083002 Jochen Küpper and Stephan Stern and Lotte Holmegaard and Frank Filsinger and Arnaud Rouzée and Artem Rudenko and Per Johnsson and Andrew V. Martin and Marcus Adolph and Andrew Aquila and Saša Bajt and Anton Barty and Christoph Bostedt and John …

X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

19 Dec 2018 | BioXFEL Publications | Contributor(s): Scott C. Jensen, Brendan Sullivan, Daniel A. Hartzler, Jose Meza Aguilar, Salah Awel, Saša Bajt, Shibom Basu, Richard Bean, Henry Chapman, Chelsie E Conrad, Matthias Frank, Raimund Fromme, Jose M. Martin-Garcia, Thomas D. Grant, Michael Heymann, Mark S. Hunter, Gihan Kaushylal Ketawala, Richard Kirian, Juraj Knoska, Christopher Kupitz, Xuanxuan Li, Mengning Liang, Stella Lisova, Valerio Mariani, Victoria Mazalova, Marc Messerschmidt, Michael Moran, Garrett Charles Nelson, Dominik Oberthür, Alex Schaffer, Raymond G. Sierra, Natalie Vaughn, Uwe Weierstall, Max Oliver Wiedorn, P. Lourdu Xavier, Jay-How Yang, Oleksandr Yefanov, Nadia Zatsepin, Andrew Aquila, Petra Fromme, Sébastien Boutet, Gerald T. Seidler, Yulia Pushkar

http://dx.doi.org/10.1021/acs.jpclett.8b03595 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Jensen, S.C. et al., 2019. X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. The …

X-ray focusing with efficient high-NA multilayer Laue lenses

23 Mar 2018 | BioXFEL Publications | Contributor(s): Saša Bajt, Mauro Prasciolu, Holger Fleckenstein, Martin Domaracký, Henry Chapman, Andrew J Morgan, Oleksandr Yefanov, Marc Messerschmidt, Yang Du, Kevin T Murray, Valerio Mariani, Manuela Kuhn, Steven Aplin, Kanupriya Pande, Pablo Villanueva-Perez, Karolina Stachnik, Joe Chen, Andrzej Andrejczuk, Alke Meents, Anja Burkhardt, David Pennicard, Xiaojing Huang, Hanfei Yan, Evgeny Nazaretski, Yong S Chu, Christian E Hamm

http://dx.doi.org/10.1038/lsa.2017.162 journal-article Bajt, S. et al., 2017. X-ray focusing with efficient high-NA multilayer Laue lenses. Light: Science & Applications, 7(3), p.17162. Available at: http://dx.doi.org/10.1038/lsa.2017.162. Saša Bajt and Mauro Prasciolu and Holger Fleckenstein …

X-ray Free Electron Lasers

27 Dec 2018 | BioXFEL Publications

http://dx.doi.org/10.1007/978-3-030-00551-1 book Boutet, S., Fromme, P. & Hunter, M.S. eds., 2018. X-ray Free Electron Lasers. Available at: http://dx.doi.org/10.1007/978-3-030-00551-1.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

11 Apr 2016 | BioXFEL Publications | Contributor(s): X. Edward Zhou, Xiang Gao, Anton Barty, Yanyong Kang, Yuanzheng He, Wei Liu, Andrii Ishchenko, Thomas A. White, Oleksandr Yefanov, Gye Won Han, Qingping Xu, Parker W. De Waal, Kelly M. Suino-Powell, Sébastien Boutet, Garth J. Williams, Meitian Wang, Dianfan Li, Martin Caffrey, Henry Chapman, John Spence, Petra Fromme, Uwe Weierstall, Raymond C. Stevens, Vadim Cherezov, Karsten Melcher, H. Eric Xu

http://dx.doi.org/10.1038/sdata.2016.21 X. Edward Zhou and Xiang Gao and Anton Barty and Yanyong Kang and Yuanzheng He and Wei Liu and Andrii Ishchenko and Thomas A. White and Oleksandr Yefanov and Gye Won Han and Qingping Xu and Parker W. de Waal and Kelly M. Suino-Powell and Sébastien Boutet and …

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene

09 Sep 2016 | BioXFEL Publications | Contributor(s): Brian Abbey, Ruben A. Dilanian, Connie Darmanin, Rebecca A. Ryan, Corey T. Putkunz, Andrew V. Martin, David Wood, Victor Streltsov, Michael W. M. Jones, Naylyn Gaffney, Felix Hofmann, Garth J. Williams, Sébastien Boutet, Marc Messerschmidt, M. Marvin Seibert, Sophie Williams, Evan Curwood, Eugeniu Balaur, Andrew G. Peele, Keith A. Nugent, Harry M. Quiney

http://dx.doi.org/10.1126/sciadv.1601186 Brian Abbey and Ruben A. Dilanian and Connie Darmanin and Rebecca A. Ryan and Corey T. Putkunz and Andrew V. Martin and David Wood and Victor Streltsov and Michael W. M. Jones and Naylyn Gaffney and Felix Hofmann and Garth J. Williams and Sébastien Boutet …

X-ray lasers and crystallography

29 Apr 2014 | BioXFEL Publications | Contributor(s): John Spence

journal-article http://dx.doi.org/10.1107/s2052252514009567 Spence, J.C.H., 2014. X-ray lasers and crystallography. IUCrJ, 1(3), pp.151–152. Available at: http://dx.doi.org/10.1107/s2052252514009567. John C.H. Spence

X-Ray Lasers in Biology

24 Apr 2017 | BioXFEL Publications | Contributor(s): John Spence

http://dx.doi.org/10.1016/bs.aiep.2017.01.008 book-chapter NSF-STC Biology with X-ray Lasers (NSF-1231306) Spence, J.C.H., 2017. X-Ray Lasers in Biology. Advances in Imaging and Electron Physics, pp.103–152. Available at: http://dx.doi.org/10.1016/bs.aiep.2017.01.008. John C.H. Spence

X-ray scattering exhibits time-resolved view of rhodopsin activation

10 Feb 2023 | BioXFEL Publications | Contributor(s): C. Swathi K. Menon, Konstantinos Karpos, Thomas D. Grant, Andrey V. Struts, Steven D.E. Fried, Suchithranga M.D.C. Perera, Irina V. Kosheleva, Leslie Salas-Estrada, Alan Grossfield, Petra Fromme, Richard Kirian, Michael F. Brown

http://dx.doi.org/10.1016/j.bpj.2022.11.1170 journal-article Menon, C. S. K., Karpos, K., Grant, T. D., Struts, A. V., Fried, S. D. E., Perera, S. M. D. C., Kosheleva, I. V., Salas-Estrada, L., Grossfield, A., Fromme, P., Kirian, R. A., & Brown, M. F. (2023). X-ray scattering exhibits …

X-ray two-photon absorption with high fluence XFEL pulses

07 Sep 2015 | BioXFEL Publications | Contributor(s): J Hoszowska, J Szlachetko, J-Cl Dousse, W Błachucki, Y Kayser, Ch Milne, M Pajek, S Boutet, M Messerschmidt, G Williams, C T Chantler

http://dx.doi.org/10.1088/1742-6596/635/10/102009 J Hoszowska and J Szlachetko and J-Cl Dousse and W Błachucki and Y Kayser and Ch Milne and M Pajek and S Boutet and M Messerschmidt and G Williams and C T Chantler Hoszowska, J. et al., 2015. X-ray two-photon absorption with high fluence XFEL …

X-ray-Based Techniques to Study the Nano–Bio Interface

02 Mar 2021 | BioXFEL Publications | Contributor(s): Carlos Sanchez-Cano, Ramon A. Alvarez-Puebla, John M. Abendroth, Tobias Beck, Robert Blick, Yuan Cao, Frank Caruso, Indranath Chakraborty, Henry Chapman, Chunying Chen, Bruce E. Cohen, Andre L. C. Conceição, David P. Cormode, Daxiang Cui, Kenneth A. Dawson, Gerald Falkenberg, Chunhai Fan, Neus Feliu, Mingyuan Gao, Elisabetta Gargioni, Claus-C. Glüer, Florian Grüner, Moustapha Hassan, Yong Hu, Yalan Huang, Samuel Huber, Nils Huse, Yanan Kang, Ali Khademhosseini, Thomas F. Keller, Christian Körnig, Nicholas A. Kotov, Dorota Koziej, Xing-Jie Liang, Beibei Liu, Sijin Liu, Yang Liu, Ziyao Liu, Luis M. Liz-Marzán, Xiaowei Ma, Andres Machicote, Wolfgang Maison, Adrian P. Mancuso, Saad Megahed, Bert Nickel, Ferdinand Otto, Cristina Palencia, Sakura Pascarelli, Arwen Pearson, Oula Peñate-Medina, Bing Qi, Joachim Rädler, Joseph J. Richardson, Axel Rosenhahn, Kai Rothkamm, Michael Rübhausen, Milan K. Sanyal, Raymond E. Schaak, Heinz-Peter Schlemmer, Marius Schmidt, Oliver Schmutzler, Theo Schotten, Florian Schulz, A. K. Sood, Kathryn M. Spiers, Theresa Staufer, Dominik M. Stemer, Andreas Stierle, Xing Sun, Gohar Tsakanova, Paul S. Weiss, Horst Weller, Fabian Westermeier, Ming Xu, Huijie Yan, Yuan Zeng, Ying Zhao, Yuliang Zhao, Dingcheng Zhu, Ying Zhu, Wolfgang J. Parak

http://dx.doi.org/10.1021/acsnano.0c09563 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sanchez-Cano, C. et al., 2021. X-ray-Based Techniques to Study the Nano–Bio Interface. ACS Nano, 15(3), pp.3754–3807. Available at: http://dx.doi.org/10.1021/acsnano.0c09563. Carlos …

XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia

09 Mar 2020 | BioXFEL Publications | Contributor(s): James D Zook, Mrinal Shekhar, Debra Hansen, Chelsie E Conrad, Thomas Grant, Chitrak Gupta, Thomas White, Anton Barty, Shibom Basu, Yun Zhao, Nadia Zatsepin, Andrii Ishchenko, Alex Batyuk, Cornelius Gati, Chufeng Li, Lorenzo Galli, Jesse David Coe, Mark S. Hunter, Meng Liang, Uwe Weierstall, Garret Nelson, Daniel James, Benjamin Stauch, Felicia Craciunescu, Darren Gary Thifault, Wei Liu, Vadim Cherezov, Abhishek Singharoy, Petra Fromme

http://dx.doi.org/10.1016/j.str.2020.02.005 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Zook, J. et al., 2020. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure. Available at: …

XFEL data analysis for structural biology

21 Jul 2016 | BioXFEL Publications | Contributor(s): Haiguang Liu, John Spence

http://dx.doi.org/10.1007/s40484-016-0076-z Haiguang Liu and John C. H. Spence Liu, H. & Spence, J.C.H., 2016. XFEL data analysis for structural biology. Quantitative Biology, 4(3), pp.159–176. Available at: http://dx.doi.org/10.1007/s40484-016-0076-z. NSF-STC Biology with X-ray Lasers …

XFEL Game - Windows Download

25 Oct 2016 | Downloads | Contributor(s): fiacre

Windows Version

XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

24 Apr 2019 | BioXFEL Publications | Contributor(s): Linda C. Johansson, Benjamin Stauch, John D. McCorvy, Gye Won Han, Nilkanth N Patel, Xi-Ping Huang, Alexander Batyuk, Cornelius Gati, Samuel T. Slocum, Chufeng Li, Jessica M. Grandner, Shuming Hao, Reid H. J. Olsen, Alexandra R. Tribo, Sahba Zaare, Lan Zhu, Nadia Zatsepin, Uwe Weierstall, Saïd Yous, Raymond C. Stevens, Wei Liu, Bryan L. Roth, Vsevolod Katritch, Vadim Cherezov

http://dx.doi.org/10.1038/s41586-019-1144-0 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Johansson, L.C. et al., 2019. XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. Nature. Available at: http://dx.doi.org/10.1038/s41586-019-1144-0. …

XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction

19 Dec 2017 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Rahel Woldeyes, Takanori Nakane, Kotaro Koiwai, Ayumi Yamashita, Tomoyuki Tanaka, Toshi Arima, Jun Kobayashi, Tetsuya Masuda, Mamoru Suzuki, Michihiro Sugahara, Rie Tanaka, Eriko Nango, So Iwata, Fumiaki Yumoto, James Fraser, William F. DeGrado

http://dx.doi.org/10.1107/s0108767317099603 journal-article Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction. Acta Crystallographica Section A Foundations and Advances, 73(a1), …

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

23 Aug 2017 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Rahel Woldeyes, Takanori Nakane, Ayumi Yamashita, Tomoyuki Tanaka, Kotaro Koiwai, Aaron S. Brewster, Benjamin A. Barad, Yujie Chen, Thomas Lemmin, Monarin Uervirojnangkoorn, Toshi Arima, Jun Kobayashi, Tetsuya Masuda, Mamoru Suzuki, Michihiro Sugahara, Nicholas K. Sauter, Rie Tanaka, Osamu Nureki, Kensuke Tono, Yasumasa Joti, Eriko Nango, So Iwata, Fumiaki Yumoto, James Fraser, William F. DeGrado

http://dx.doi.org/10.1073/pnas.1705624114 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Thomaston, J.L. et al., 2017. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proceedings of the National Academy of …

XFELs for structure and dynamics in biology

10 May 2017 | BioXFEL Publications | Contributor(s): J. C. H. Spence

http://dx.doi.org/10.1107/s2052252517005760 The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are …

XFELs open a new era in structural chemical biology

17 Nov 2015 | BioXFEL Publications | Contributor(s): Petra Fromme

http://dx.doi.org/10.1038/nchembio.1968 Petra Fromme Fromme, P., 2015. XFELs open a new era in structural chemical biology. Nat Chem Biol, 11(12), pp.895–899. Available at: http://dx.doi.org/10.1038/nchembio.1968. NSF-STC Biology with X-ray Lasers (NSF-1231306) journal-article

XRayView

09 Oct 2014 | Downloads | Contributor(s): George Phillips

XRayView : A Virtual X-Ray Crystallography Laboratory This software uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, …

Zatsepin_IUCr2015_SFX_software.pdf

21 Jul 2015 | PDF

Zatsepin_IUCr2015_SFX_software.pdf