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  1. Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity

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    30 Aug 2020 | BioXFEL Publications | Contributor(s): Josué A. Benjamín-Rivera, Andrés E. Cardona-Rivera, Ángel L. Vázquez-Maldonado, Christian Y. Dones-Lassalle, Héctor L. Pabón-Colon, Héctor M. Rodríguez-Rivera, Israel Rodriguez, Jean C. González-Espiet, Jessika Pazol, Jobaniel D. Pérez-Ríos, José F. Catala-Torres, Marielie Carrasquillo Rivera, Michael G. De Jesus-Soto, Nicolle A. Cordero-Virella, Paola M. Cruz-Maldonado, Patricia González-Pagan, Raul Hernández-Ríos, Kavita Gaur, Sergio A. Loza-Rosas, Arthur Tinoco

    http://dx.doi.org/10.3390/inorganics8090048 Serum transferrin (sTf) plays a pivotal role in regulating iron biodistribution and homeostasis within the body. The molecular details of sTf Fe(III) binding blood transport, and cellular delivery through transferrin receptor-mediated endocytosis are …

  2. Exploring Titanium(IV) Complexes as Potential Antimicrobial Compounds

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    26 Jan 2022 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Lauren Fernández-Vega, Andrea N. Maser-Figueroa, Branlee Sang, Patricia González-Pagán, Arthur Tinoco

    http://dx.doi.org/10.3390/antibiotics11020158 Due to the rapid mutation of pathogenic microorganisms, drug-resistant superbugs have evolved. Antimicrobial-resistant germs may share their resistance genes with other germs, making them untreatable. The search for more combative antibiotic compounds …

  3. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

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    05 May 2015 | BioXFEL Publications | Contributor(s): Daniel A Keedy, James Fraser, Henry Van Den Bedem

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated …

  4. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

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    27 Oct 2015 | BioXFEL Publications | Contributor(s): Daniel A. Keedy, James Fraser, Henry Van Den Bedem

    http://dx.doi.org/10.1371/journal.pcbi.1004507 Daniel A. Keedy and James S. Fraser and Henry van den Bedem Keedy, D.A., Fraser, J.S. & van den Bedem, H., 2015. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit A. Shehu, ed. PLoS Comput Biol, 11(10), p.e1004507. …

  5. Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles

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    25 Mar 2016 | BioXFEL Publications | Contributor(s): Matthew Coleman, Jenny A. Cappuccio, Craig D. Blanchette, Tingjuan Gao, Erin S. Arroyo, Angela K. Hinz, Feliza A. Bourguet, Brent W. Segelke, Paul D. Hoeprich, Thomas Huser, Ted A. Laurence, Vladimir L. Motin, Brett A. Chromy

    http://dx.doi.org/10.1371/journal.pone.0150166 Matthew A. Coleman and Jenny A. Cappuccio and Craig D. Blanchette and Tingjuan Gao and Erin S. Arroyo and Angela K. Hinz and Feliza A. Bourguet and Brent Segelke and Paul D. Hoeprich and Thomas Huser and Ted A. Laurence and Vladimir L. Motin and Brett …

  6. Expression and purification of an engineered human endothelin receptor B in a monomeric form

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    19 May 2016 | BioXFEL Publications | Contributor(s): A. V. Mishin, A. P. Luginina, A. P. Potapenko, V. I. Borshchevskiy, V. Katritch, E. Edelweiss, I. S. Okhrimenko, V. I. Gordeliy, V. G. Cherezov

    journal-article http://dx.doi.org/10.1134/s1607672916020216 Mishin, A.V. et al., 2016. Expression and purification of an engineered human endothelin receptor B in a monomeric form. Doklady Biochemistry and Biophysics, 467(1), pp.157–161. Available at: …

  7. Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies

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    08 Apr 2015 | BioXFEL Publications | Contributor(s): David J. Aceti, Craig A. Bingman, Russell L. Wrobel, Ronnie O. Frederick, Shin-ichi Makino, Karl W. Nichols, Sarata C. Sahu, Lai F. Bergeman, Paul G. Blommel, Claudia C. Cornilescu, Katarzyna A. Gromek, Kory D. Seder, Soyoon Hwang, John G. Primm, Grzegorz Sabat, Frank C. Vojtik, Brian F. Volkman, Zsolt Zolnai, George Phillips, John L. Markley, Brian G. Fox

    http://dx.doi.org/10.1007/s10969-015-9198-1 David J. Aceti and Craig A. Bingman and Russell L. Wrobel and Ronnie O. Frederick and Shin-ichi Makino and Karl W. Nichols and Sarata C. Sahu and Lai F. Bergeman and Paul G. Blommel and Claudia C. Cornilescu and Katarzyna A. Gromek and Kory D. Seder and …

  8. Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1

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    19 Aug 2014 | BioXFEL Publications | Contributor(s): Ho-Hsien Lee, Irene Cherni, HongQi Yu, Raimund Fromme, Jeffrey D. Doran, Ingo Grotjohann, Michele Mittman, Shibom Basu, Arpan Deb, Katerina Dörner, Andrew Aquila, Anton Barty, Sébastien Boutet, Henry Chapman, R. Bruce Doak, Mark S. Hunter, Daniel James, Richard Kirian, Christopher Kupitz, Robert M Lawrence, Haiguang Liu, Karol Nass, Ilme Schlichting, Kevin E. Schmidt, M. Marvin Seibert, Robert L. Shoeman, John Spence, Francesco Stellato, Uwe Weierstall, Garth J. Williams, Chunhong Yoon, Dingjie Wang, Nadia Zatsepin, Brenda Hogue, Nobuyuki Matoba, Petra Fromme, Tsafrir S. Mor

    CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein ofHuman immunodeficiency virus 1(HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral …

  9. Extended asymmetric-cut multilayer X-ray gratings

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    01 Jun 2015 | BioXFEL Publications | Contributor(s): Mauro Prasciolu, Anton Haase, Frank Scholze, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1364/oe.23.015195 Mauro Prasciolu and Anton Haase and Frank Scholze and Henry N. Chapman and Saša Bajt Prasciolu, M. et al., 2015. Extended asymmetric-cut multilayer X-ray gratings. Optics Express, 23(12), p.15195. Available at: http://dx.doi.org/10.1364/oe.23.015195. …

  10. Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range

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    23 Nov 2020 | BioXFEL Publications | Contributor(s): Mohamed Abdellatif-Youssef, Martin Etter, Petra Fromme, Marco Salerno

    http://dx.doi.org/10.1016/j.jmmm.2020.167574 journal-article Abdellatif-Youssef, M. et al., 2021. Extended properties of magnetic spins of zinc ferrite nanoparticles in the THz frequency range. Journal of Magnetism and Magnetic Materials, 525, p.167574. Available at: …

  11. Extracting conformational heterogeneity from 2D and 3D cryo-EM data

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    08 Feb 2024 | BioXFEL Publications | Contributor(s): Samuel Hoff, Massimiliano Bonomi, James Fraser, Eric Greene

    http://dx.doi.org/10.1016/j.bpj.2023.11.376 journal-article Hoff, S., Bonomi, M., Fraser, J., & Greene, E. (2024). Extracting conformational heterogeneity from 2D and 3D cryo-EM data. Biophysical Journal, 123(3), 50a–51a. https://doi.org/10.1016/j.bpj.2023.11.376 Samuel Hoff and Massimiliano …

  12. Extracting water and ion distributions from solution x-ray scattering experiments

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    03 Jun 2016 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Lois Pollack, David Case

    http://dx.doi.org/10.1063/1.4953037 journal-article Nguyen, H.T. et al., 2016. Extracting water and ion distributions from solution x-ray scattering experiments. The Journal of Chemical Physics, 144(21), p.214105. Available at: http://dx.doi.org/10.1063/1.4953037. Hung T. Nguyen and Suzette A. …

  13. Extraction of fast changes in the structure of a disordered ensemble of photoexcited biomolecules

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    13 Oct 2015 | Teaching Materials

    Using pump-probe experiments of varying time intervals between pump and probe, the method of time-resolved crystallography has given many insights into the fast time variations of crystallized molecules as a result of photoexcitation. We show here that quantities extractable from multiple …

  14. Fabrication of wedged multilayer Laue lenses

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    12 Mar 2015 | BioXFEL Publications | Contributor(s): M. Prasciolu, A. F. G. Leontowich, J. Krzywinski, A. Andrejczuk, H. N. Chapman, S. Bajt

    http://dx.doi.org/10.1364/ome.5.000748 M. Prasciolu and A. F. G. Leontowich and J. Krzywinski and A. Andrejczuk and H. N. Chapman and S. Bajt Prasciolu, M. et al., 2015. Fabrication of wedged multilayer Laue lenses. Opt. Mater. Express, 5(4), p.748. Available at: …

  15. Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): Alexander L. Van Slyke, Juan Wang, Avtar Singh, Lois Pollack, Warren R. Zipfel

    http://dx.doi.org/10.1016/j.bpj.2013.11.4364 journal-article Van Slyke, A.L. et al., 2014. Fast Binding Kinetics of RNA Aptamers Measured using a Novel Microfluidic Mixer. Biophysical Journal, 106(2), p.796a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.4364. Alexander L. Van Slyke and …

  16. Fast k-NNG Construction with GPU-Based Quick Multi-Select

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    08 May 2014 | BioXFEL Publications | Contributor(s): Ivan Komarov, Ali Dashti, Roshan M. D'Souza

    http://dx.doi.org/10.1371/journal.pone.0092409 journal-article Komarov, I., Dashti, A. & D’Souza, R.M., 2014. Fast k-NNG Construction with GPU-Based Quick Multi-Select M. Gomez-Gesteira, ed. PLoS ONE, 9(5), p.e92409. Available at: http://dx.doi.org/10.1371/journal.pone.0092409. Ivan Komarov …

  17. FBXW8-dependent degradation of MRFAP1 in anaphase controls mitotic cell death

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    16 Oct 2017 | BioXFEL Publications | Contributor(s): Duan-Zhuo Li, Shun-Fang Liu, Lan Zhu, Yu-Xing Wang, Yi-Xiang Chen, Jie Liu, Gang Hu, Xin Yu, Jian Li, Jin Zhang, Zhi-Xiang Wu, Han Lu, Wei Liu, Bin Liu

    http://dx.doi.org/10.18632/oncotarget.21843 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, D.-Z. et al., 2017. FBXW8-dependent degradation of MRFAP1 in anaphase controls mitotic cell death. Oncotarget, 8(57). Available at: http://dx.doi.org/10.18632/oncotarget.21843. …

  18. FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

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    07 Jul 2017 | BioXFEL Publications | Contributor(s): Kenneth R. Beyerlein, Thomas A. White, Oleksandr Yefanov, Cornelius Gati, Ivan G. Kazantsev, Nicolai Fog-Gade Nielsen, Peter M. Larsen, Henry Chapman, Søren Schmidt

    http://dx.doi.org/10.1107/s1600576717007506 A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which …

  19. Femtosecond and nanometre visualization of structural dynamics in superheated nanoparticles

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    25 Jan 2016 | BioXFEL Publications | Contributor(s): Tais Gorkhover, Sebastian Schorb, Ryan Coffee, Marcus Adolph, Lutz Foucar, Daniela Rupp, Andrew Aquila, John D. Bozek, Sascha W. Epp, Benjamin Erk, Lars Gumprecht, Lotte Holmegaard, Andreas Hartmann, Robert Hartmann, Günter Hauser, Peter Holl, Andre Hömke, Per Johnsson, Nils Kimmel, Kai-Uwe Kühnel, Marc Messerschmidt, Christian Reich, Arnaud Rouzée, Benedikt Rudek, Carlo Schmidt, Joachim Schulz, Heike Soltau, Stephan Stern, Georg Weidenspointner, Bill White, Jochen Küpper, Lothar Strüder, Ilme Schlichting, Joachim Ullrich, Daniel Rolles, Artem Rudenko, Thomas Möller, Christoph Bostedt

    http://dx.doi.org/10.1038/nphoton.2015.264 Tais Gorkhover and Sebastian Schorb and Ryan Coffee and Marcus Adolph and Lutz Foucar and Daniela Rupp and Andrew Aquila and John D. Bozek and Sascha W. Epp and Benjamin Erk and Lars Gumprecht and Lotte Holmegaard and Andreas Hartmann and Robert Hartmann …

  20. Femtosecond crystallography of membrane proteins in the lipidic cubic phase

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): W. Liu, D. Wacker, C. Wang, E. Abola, V. Cherezov

    http://dx.doi.org/10.1098/rstb.2013.0314 W. Liu and D. Wacker and C. Wang and E. Abola and V. Cherezov Liu, W. et al., 2014. Femtosecond crystallography of membrane proteins in the lipidic cubic phase. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), …

  21. Femtosecond profiling of shaped x-ray pulses

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    08 Mar 2018 | BioXFEL Publications | Contributor(s): M C Hoffmann, I Grguraš, C Behrens, C Bostedt, J Bozek, H Bromberger, R Coffee, J T Costello, L F DiMauro, Y Ding, G Doumy, W Helml, M Ilchen, R Kienberger, S Lee, A R Maier, T Mazza, M Meyer, M Messerschmidt, S Schorb, W Schweinberger, K Zhang, A L Cavalieri

    http://dx.doi.org/10.1088/1367-2630/aab548 journal-article Hoffmann, M.C. et al., 2018. Femtosecond profiling of shaped x-ray pulses. New Journal of Physics, 20(3), p.033008. Available at: http://dx.doi.org/10.1088/1367-2630/aab548. M C Hoffmann and I Grguraš and C Behrens and C Bostedt and J …

  22. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses

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    12 Feb 2021 | BioXFEL Publications | Contributor(s): P. Lourdu Xavier, Kartik Ayyer, Oleksandr Yefanov, Luca Gelisio, Johan Bielecki, Amit K. Samanta, Saša Bajt, Ruojie Sha, David Bushnell, Roger Kornberg, Yevheniy Ovcharenko, Jochen Kuepper, Michael Meyer, Nadrian C. Seeman, Henry Chapman

    http://dx.doi.org/10.1016/j.bpj.2020.11.1697 journal-article Xavier, P.L. et al., 2021. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophysical Journal, 120(3), p.265a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1697. P. …

  23. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

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    05 May 2016 | BioXFEL Publications | Contributor(s): K. Pande, C. D. M. Hutchison, G. Groenhof, A. Aquila, J. S. Robinson, J. Tenboer, S. Basu, S. Boutet, D. P. DePonte, M. Liang, T. A. White, N. A. Zatsepin, O. Yefanov, D. Morozov, D. Oberthuer, C. Gati, G. Subramanian, D. James, Y. Zhao, J. Koralek, J. Brayshaw, C. Kupitz, C. Conrad, S. Roy-Chowdhury, J. D. Coe, M. Metz, P. L. Xavier, T. D. Grant, J. E. Koglin, G. Ketawala, R. Fromme, V.  rajer, R. Henning, J. C. H. Spence, A. Ourmazd, P. Schwander, U. Weierstall, M. Frank, P. Fromme, A. Barty, H. N. Chapman, K. Moffat, J. J. Van Thor, M. Schmidt

    http://dx.doi.org/10.1126/science.aad5081 K. Pande and C. D. M. Hutchison and G. Groenhof and A. Aquila and J. S. Robinson and J. Tenboer and S. Basu and S. Boutet and D. P. DePonte and M. Liang and T. A. White and N. A. Zatsepin and O. Yefanov and D. Morozov and D. Oberthuer and C. Gati and G. …

  24. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser

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    18 May 2020 | BioXFEL Publications | Contributor(s): Tokushi Sato, Romain Letrun, Henry J. Kirkwood, Jia Liu, Patrik Vagovič, Grant Mills, Yoonhee Kim, Cedric M. S. Takem, Marc Planas, Moritz Emons, Tomasz Jezynski, Guido Palmer, Max Lederer, Sebastian Schulz, Jost Mueller, Holger Schlarb, Alessandro Silenzi, Gabriele Giovanetti, Andrea Parenti, Martin Bergemann, Thomas Michelat, Janusz Szuba, Jan Grünert, Henry Chapman, Adrian P. Mancuso

    http://dx.doi.org/10.1364/optica.396728 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sato, T. et al., 2020. Femtosecond timing synchronization at megahertz repetition rates for an x-ray free-electron laser. Optica, 7(6), p.716. Available at: …

  25. Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene

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    03 May 2018 | BioXFEL Publications | Contributor(s): Carolin Seuring, Kartik Ayyer, Eleftheria Filippaki, Miriam Barthelmess, Jean-Nicolas Longchamp, Philippe Ringler, Tommaso Pardini, David H. Wojtas, Matthew Coleman, Katerina Dörner, Silje Fuglerud, Greger Hammarin, Birgit Habenstein, Annette E. Langkilde, Antoine Loquet, Alke Meents, Roland Riek, Henning Stahlberg, Sébastien Boutet, Mark S. Hunter, Jason Koglin, Mengning Liang, Helen M. Ginn, Rick P. Millane, Matthias Frank, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1038/s41467-018-04116-9 journal-article Seuring, C. et al., 2018. Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene. Nature Communications, 9(1). Available at: http://dx.doi.org/10.1038/s41467-018-04116-9. Carolin Seuring and Kartik …

  26. Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals

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    26 Jan 2018 | BioXFEL Publications | Contributor(s): Salah Awel, Richard Kirian, Max Oliver Wiedorn, Kenneth R. Beyerlein, Nils Roth, Daniel A. Horke, Dominik Oberthür, Juraj Knoska, Valerio Mariani, Andrew Morgan, Luigi Adriano, Alexandra Tolstikova, P. Lourdu Xavier, Oleksandr Yefanov, Andrew Aquila, Anton Barty, Shatabdi Roy-Chowdhury, Mark S. Hunter, Daniel James, Joseph S. Robinson, Uwe Weierstall, Andrei V. Rode, Saša Bajt, Jochen Küpper, Henry Chapman

    http://dx.doi.org/10.1107/s1600576717018131 High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles …

  27. Femtosecond X-ray diffraction from two-dimensional protein crystals

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    10 Feb 2014 | BioXFEL Publications | Contributor(s): Matthias Frank, David B. Carlson, Mark S. Hunter, Garth J. Williams, Marc Messerschmidt, Nadia Zatsepin, Anton Barty, W. Henry Benner, Kaiqin Chu, Alexander T. Graf, Stefan Hau-Riege, Richard Kirian, Celestino Padeste, Tommaso Pardini, Bill Pedrini, Brent W. Segelke, M. Marvin Seibert, John Spence, Ching-Ju Tsai, Stephen M. Lane, Xiao-Dan Li, Gebhard F.X. Schertler, Sebastien Boutet, Matthew Coleman, James E. Evans

    X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to …

  28. Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles

    0.0 out of 5 stars 

    16 Feb 2018 | BioXFEL Publications | Contributor(s): Tais Gorkhover, Anatoli Ulmer, Ken Ferguson, Max Bucher, Filipe R. N. C. Maia, Johan Bielecki, Tomas Ekeberg, Max F. Hantke, Benedikt J. Daurer, Carl Nettelblad, Jakob Andreasson, Anton Barty, Petr Bruza, Sebastian Carron, Dirk Hasse, Jacek Krzywinski, Daniel S. D. Larsson, Andrew Morgan, Kerstin Mühlig, Maria Müller, Kenta Okamoto, Alberto Pietrini, Daniela Rupp, Mario Sauppe, Gijs Van Der Schot, Marvin Seibert, Jonas A. Sellberg, Martin Svenda, Michelle Swiggers, Nicusor Timneanu, Daniel Westphal, Garth Williams, Alessandro Zani, Henry Chapman, Gyula Faigel, Thomas Möller, Janos Hajdu, Christoph Bostedt

    http://dx.doi.org/10.1038/s41566-018-0110-y journal-article Gorkhover, T. et al., 2018. Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles. Nature Photonics, 12(3), pp.150–153. Available at: http://dx.doi.org/10.1038/s41566-018-0110-y. Tais Gorkhover and Anatoli Ulmer …

  29. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules

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    10 Jun 2014 | BioXFEL Publications | Contributor(s): D Rolles, R Boll, M Adolph, A Aquila, C Bostedt, J D Bozek, H N Chapman, R Coffee, N Coppola, P Decleva, T Delmas, S W Epp, B Erk, F Filsinger, L Foucar, L Gumprecht, A Hömke, T Gorkhover, L Holmegaard, P Johnsson, Ch Kaiser, F Krasniqi, K-U Kühnel, J Maurer, M Messerschmidt, R Moshammer, W Quevedo, I Rajkovic, A Rouzée, B Rudek, I Schlichting, C Schmidt, S Schorb, C D Schröter, J Schulz, H Stapelfeldt, M Stener, S Stern, S Techert, J Thøgersen, M J J Vrakking, A Rudenko, J Küpper, J Ullrich

    http://dx.doi.org/10.1088/0953-4075/47/12/124035 journal-article Rolles, D. et al., 2014. Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules. Journal of Physics B: Atomic, Molecular and Optical Physics, 47(12), p.124035. Available at: …

  30. Few-fs resolution of a photoactive protein traversing a conical intersection

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    03 Nov 2021 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, N. Breckwoldt, R. Fung, R. Sepehr, M. Schmidt, P. Schwander, R. Santra, A. Ourmazd

    http://dx.doi.org/10.1038/s41586-021-04050-9 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Hosseinizadeh, A. et al., 2021. Few-fs resolution of a photoactive protein traversing a conical intersection. Nature, 599(7886), pp.697–701. Available at: …

  31. Fiber Diffraction without Fibers

    0.0 out of 5 stars 

    27 Jun 2013 | BioXFEL Publications | Contributor(s): H.-C. Poon, P. Schwander, M. Uddin, D. K. Saldin

    http://dx.doi.org/10.1103/physrevlett.110.265505 journal-article Poon, H.-C. et al., 2013. Fiber Diffraction without Fibers. Physical Review Letters, 110(26). Available at: http://dx.doi.org/10.1103/physrevlett.110.265505. H.-C. Poon and P. Schwander and M. Uddin and D. K. Saldin

  32. Field dependence of cross relaxation in scandium (I=7/2)

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    03 Sep 2003 | BioXFEL Publications | Contributor(s): L. Pollack, E.N. Smith, R.C. Richardson

    https://doi.org/10.1016/0921-4526(94)90501-0 journal-article Pollack, L., Smith, E. N., & Richardson, R. C. (1994). Field dependence of cross relaxation in scandium (I=7/2). Physica B: Condensed Matter, 194–196, 343–344. https://doi.org/10.1016/0921-4526(94)90501-0 L. Pollack and E.N. Smith …

  33. Filling data analysis gaps in time-resolved crystallography by machine learning

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    21 Jan 2025 | BioXFEL Publications | Contributor(s): Justin Trujillo, Russell Fung, Madan Kumar Shankar, Peter Schwander, Ahmad Hosseinizadeh

    https://doi.org/10.1063/4.0000280 There is a growing understanding of the structural dynamics of biological molecules fueled by x-ray crystallography experiments. Time-resolved serial femtosecond crystallography (TR-SFX) with x-ray Free Electron Lasers allows the measurement of ultrafast structural …

  34. First Annual NSF Site Visit Photo

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    23 Jun 2014 | Downloads | Contributor(s): Edward J Sobczak

    The BioXFEL Center meets at Hauptman-Woodward in Buffalo for its first annual NSF site visit.

  35. First Experiments in Structural Biology at the European X-ray Free-Electron Laser

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    25 May 2020 | BioXFEL Publications | Contributor(s): Grant Mills, Richard Bean, Adrian P. Mancuso

    http://dx.doi.org/10.3390/app10103642 Ultrabright pulses produced in X-ray free-electron lasers (XFELs) offer new possibilities for industry and research, particularly for biochemistry and pharmaceuticals. The unprecedented brilliance of these next-generation sources enables structure determination …

  36. Fixed-target protein serial microcrystallography with an x-ray free electron laser

    0.0 out of 5 stars 

    12 Aug 2014 | BioXFEL Publications | Contributor(s): Mark S. Hunter, Brent W. Segelke, Marc Messerschmidt, Garth J. Williams, Nadia Zatsepin, Anton Barty, W. Henry Benner, David B. Carlson, Matthew Coleman, Alexander Graf, Stefan Hau-Riege, Tommaso Pardini, M. Marvin Seibert, James Evans, Sébastien Boutet, Matthias Frank

    http://dx.doi.org/10.1038/srep06026 Mark S. Hunter and Brent Segelke and Marc Messerschmidt and Garth J. Williams and Nadia A. Zatsepin and Anton Barty and W. Henry Benner and David B. Carlson and Matthew Coleman and Alexander Graf and Stefan P. Hau-Riege and Tommaso Pardini and M. Marvin Seibert …

  37. Flavin reduction activates Drosophila cryptochrome

    0.0 out of 5 stars 

    02 Dec 2013 | BioXFEL Publications | Contributor(s): A. T. Vaidya, D. Top, C. C. Manahan, J. M. Tokuda, S. Zhang, L. Pollack, M. W. Young, B. R. Crane

    http://dx.doi.org/10.1073/pnas.1313336110 journal-article Vaidya, A.T. et al., 2013. Flavin reduction activates Drosophila cryptochrome. Proceedings of the National Academy of Sciences, 110(51), pp.20455–20460. Available at: http://dx.doi.org/10.1073/pnas.1313336110. A. T. Vaidya and D. Top …

  38. Flexibility and design: conformational heterogeneity along the evolutionary trajectory of a redesigned ubiquitin

    0.0 out of 5 stars 

    19 Oct 2016 | BioXFEL Publications | Contributor(s): Justin T Biel, Michael Thompson, Christian N Cunningham, Jacob E Corn, James Fraser

    http://dx.doi.org/10.1101/081646 Although protein design has been used to introduce new functions, designed variants generally only function as well as natural proteins after rounds of laboratory evolution. One possibility for this pattern is that designed mutants frequently sample nonfunctional …

  39. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin

    0.0 out of 5 stars 

    13 Apr 2017 | BioXFEL Publications | Contributor(s): Justin T. Biel, Michael Thompson, Christian N. Cunningham, Jacob E. Corn, James Fraser

    http://dx.doi.org/10.1016/j.str.2017.03.009 journal-article Biel, J.T. et al., 2017. Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure, 25(5), pp.739–749.e3. Available at: http://dx.doi.org/10.1016/j.str.2017.03.009. …

  40. Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations

    0.0 out of 5 stars 

    18 Feb 2013 | BioXFEL Publications | Contributor(s): Noah Ollikainen, Colin A. Smith, James Fraser, Tanja Kortemme

    http://dx.doi.org/10.1016/b978-0-12-394292-0.00004-7 book-chapter Ollikainen, N. et al., 2013. Flexible Backbone Sampling Methods to Model and Design Protein Alternative Conformations. Methods in Protein Design, pp.61–85. Available at: http://dx.doi.org/10.1016/b978-0-12-394292-0.00004-7. Noah …

  41. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser

    0.0 out of 5 stars 

    02 Jun 2017 | BioXFEL Publications | Contributor(s): David Popp, N. Duane Loh, Habiba Zorgati, Umesh Ghoshdastider, Lu Ting Liow, Magdalena I. Ivanova, Mårten Larsson, Daniel P. DePonte, Richard Bean, Kenneth R. Beyerlein, Cornelius Gati, Dominik Oberthuer, David Arnlund, Gisela Brändén, Peter Berntsen, Duilio Cascio, Leonard M. G. Chavas, Joe Chen, Ke Ding, Holger Fleckenstein, Lars Gumprecht, Rajiv Harimoorthy, Estelle Mossou, Michael R. Sawaya, Aaron S. Brewster, Johan Hattne, Nicholas K. Sauter, Marvin Seibert, Carolin Seuring, Francesco Stellato, Thomas Tilp, David S. Eisenberg, Marc Messerschmidt, Garth J. Williams, Jason E. Koglin, Lee Makowski, Rick P. Millane, Trevor Forsyth, Sébastien Boutet, Thomas A. White, Anton Barty, Henry Chapman, Swaine L. Chen, Mengning Liang, Richard Neutze, Robert C. Robinson

    http://dx.doi.org/10.1002/cm.21378 journal-article Popp, D. et al., 2017. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton. Available at: http://dx.doi.org/10.1002/cm.21378. David Popp and N. Duane Loh and Habiba Zorgati and Umesh …

  42. Fluorescence Recovery After Photobleaching in Lipidic Cubic Phase (LCP-FRAP)

    0.0 out of 5 stars 

    22 Mar 2015 | BioXFEL Publications | Contributor(s): Gustavo Fenalti, Enrique E. Abola, Chong Wang, Beili Wu, Vadim Cherezov

    http://dx.doi.org/10.1016/bs.mie.2014.12.008 Gustavo Fenalti and Enrique E. Abola and Chong Wang and Beili Wu and Vadim Cherezov Fenalti, G. et al., 2015. Fluorescence Recovery After Photobleaching in Lipidic Cubic Phase (LCP-FRAP). Membrane Proteins—Engineering, Purification and Crystallization, …

  43. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET

    0.0 out of 5 stars 

    15 Feb 2019 | BioXFEL Publications | Contributor(s): Alex Plumridge, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1931 poster Plumridge, A. & Pollack, L., 2019. Following Folding Pathways of Common Riboswitch Motifs with Time-Resolved Single-Molecule FRET. Biophysical Journal, 116(3), p.355a. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1931. Alex Plumridge …

  44. Formation and Fate of a Complete 31-Protein RNA Polymerase II Transcription Preinitiation Complex

    0.0 out of 5 stars 

    10 Jan 2013 | BioXFEL Publications | Contributor(s): Kenji Murakami, Guillermo Calero, Christopher R. Brown, Xin Liu, Ralph E. Davis, Hinrich Boeger, Roger Kornberg

    journal-article http://dx.doi.org/10.1074/jbc.m112.433623 Murakami, K. et al., 2013. Formation and Fate of a Complete 31-Protein RNA Polymerase II Transcription Preinitiation Complex. Journal of Biological Chemistry, 288(9), pp.6325–6332. Available at: http://dx.doi.org/10.1074/jbc.m112.433623. …

  45. Four amino acids define the CO2binding pocket of enoyl-CoA carboxylases/reductases

    0.0 out of 5 stars 

    26 Jun 2019 | BioXFEL Publications | Contributor(s): Gabriele M. M. Stoffel, David Adrian Saez, Hasan Demirci, Bastian Vögeli, Yashas Rao, Jan Zarzycki, Yasuo Yoshikuni, Soichi Wakatsuki, Esteban Vöhringer-Martinez, Tobias J. Erb

    http://dx.doi.org/10.1073/pnas.1901471116 Carboxylases are biocatalysts that capture and convert carbon dioxide (CO2) under mild conditions and atmospheric concentrations at a scale of more than 400 Gt annually. However, how these enzymes bind and control the gaseous CO2molecule during catalysis is …

  46. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

    0.0 out of 5 stars 

    14 Apr 2021 | BioXFEL Publications | Contributor(s): Marion Schuller, Galen J. Correy, Stefan Gahbauer, Daren Fearon, Taiasean Wu, Roberto Efraín Díaz, Iris Diane Young, Luan Carvalho Martins, Dominique H. Smith, Ursula Schulze-Gahmen, Tristan W. Owens, Ishan Deshpande, Gregory E. Merz, Aye C. Thwin, Justin T. Biel, Jessica K. Peters, Michelle Moritz, Nadia Herrera, Huong T. Kratochvil, Anthony Aimon, James M. Bennett, Jose Brandao Neto, Aina E. Cohen, Alexandre Dias, Alice Douangamath, Louise Dunnett, Oleg Fedorov, Matteo P. Ferla, Martin R. Fuchs, Tyler J. Gorrie-Stone, James Holton, Michael G. Johnson, Tobias Krojer, George Meigs, Ailsa J. Powell, Johannes Gregor Matthias Rack, Victor L. Rangel, Silvia Russi, Rachael E. Skyner, Clyde A. Smith, Alexei S. Soares, Jennifer L. Wierman, Kang Zhu, Peter O’Brien, Natalia Jura, Alan Ashworth, John J. Irwin, Michael Thompson, Jason E. Gestwicki, Frank Von Delft, Brian K. Shoichet, James Fraser, Ivan Ahel, Ron Morganti

    http://dx.doi.org/10.1126/sciadv.abf8711 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic …

  47. framesorter

    0.0 out of 5 stars 

    20 Apr 2015 | Downloads

    Framesorter is a script for parsing the output from Cheetah  

  48. Free Electron Lasers and Crystallography

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Paul Adams (LBNL) BioXFEL in the greater context of crystallography

  49. Free-electron laser data for multiple-particle fluctuation scattering analysis

    0.0 out of 5 stars 

    02 Oct 2018 | BioXFEL Publications | Contributor(s): Kanupriya Pande, Jeffrey J. Donatelli, Erik Malmerberg, Lutz Foucar, Billy K. Poon, Markus Sutter, Sabine Botha, Shibom Basu, R. Bruce Doak, Katerina Dörner, Sascha W. Epp, Lars Englert, Raimund Fromme, Elisabeth Hartmann, Robert Hartmann, Guenter Hauser, Johan Hattne, Ahmad Hosseinizadeh, Stephan Kassemeyer, Lukas Lomb, Sebastian F. Carron Montero, Andreas Menzel, Daniel Rolles, Artem Rudenko, Marvin M. Seibert, Raymond George Sierra, Peter Schwander, Abbas Ourmazd, Petra Fromme, Nicholas K. Sauter, Michael Bogan, John Bozek, Christoph Bostedt, Ilme Schlichting, Cheryl A. Kerfeld, Petrus H. Zwart

    http://dx.doi.org/10.1038/sdata.2018.201 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Pande, K. et al., 2018. Free-electron laser data for multiple-particle fluctuation scattering analysis. Scientific Data, 5, p.180201. Available at: http://dx.doi.org/10.1038/sdata.2018.201. …

  50. FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography

    0.0 out of 5 stars 

    21 Feb 2018 | BioXFEL Publications | Contributor(s): H. Olof Jönsson, Christofer Östlin, Howard A. Scott, Henry Chapman, Steve J. Aplin, Nicuşor Tîmneanu, Carl Caleman

    http://dx.doi.org/10.1016/j.hedp.2018.02.004 journal-article Jönsson, H.O. et al., 2018. FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography. High Energy Density Physics. Available at: http://dx.doi.org/10.1016/j.hedp.2018.02.004. H. Olof Jönsson …

  51. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces

    0.0 out of 5 stars 

    09 Dec 2020 | BioXFEL Publications | Contributor(s): Ryan S. Edmonds, Tanner J. Finney, Michael R. Bull, Aude A. Watrelot, Tonya L. Kuhl

    http://dx.doi.org/10.1016/j.foodhyd.2020.106522 journal-article Edmonds, R.S. et al., 2021. Friction measurements of model saliva-wine solutions between polydimethylsiloxane surfaces. Food Hydrocolloids, 113, p.106522. Available at: http://dx.doi.org/10.1016/j.foodhyd.2020.106522. Ryan S. …

  52. From Alignment Laser to 3D Structures: Determining Structures of GPCRs in a Compact X‐ray Light Source

    0.0 out of 5 stars 

    03 May 2022 | BioXFEL Publications | Contributor(s): Gabriela Diaz‐Figueroa, Marc Messerschimdt, Jong Woo‐Kim, Tien Olson

    http://dx.doi.org/10.1096/fasebj.2022.36.s1.r3457 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Diaz‐Figueroa, G., Messerschimdt, M., Woo‐Kim, J., & Olson, T. (2022). From Alignment Laser to 3D Structures: Determining Structures of GPCRs in a Compact X‐ray Light Source. The …

  53. From cctbx to cctbx.xfel and beyond

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Johan Hattne (HHMI) Algorithms to process X-ray diffraction images into accurate atomic models of macromolecules have undergone steady refinement over the past decades. As methods by which crystallographic diffraction patters are obtained are further developed, these techniques continue to provide …

  54. From deep TLS validation to ensembles of atomic models built from elemental motions

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    02 Jan 2015 | BioXFEL Publications | Contributor(s): Alexandre Urzhumtsev, Pavel Afonine, Andrew H Van Benschoten, James Fraser, Paul D Adams

    The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In …

  55. From deep TLS validation to ensembles of atomic models built from elemental motions

    0.0 out of 5 stars 

    27 Jul 2015 | BioXFEL Publications | Contributor(s): Alexandre Urzhumtsev, Pavel V. Afonine, Andrew H. Van Benschoten, James Fraser, Paul D. Adams

    The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because theT,LandSmatrices describe a combination of …

  56. From Protein Design to the Energy Landscape of a Cold Unfolding Protein

    0.0 out of 5 stars 

    07 Feb 2022 | BioXFEL Publications | Contributor(s): Surya V. S. R. K Pulavarti, Jack B. Maguire, Shirley Yuen, Joseph S. Harrison, Jermel Griffin, Lakshmanane Premkumar, Edward A. Esposito, George I. Makhatadze, Angel E. Garcia, Thomas M. Weiss, Edward Snell, Brian Kuhlman, Thomas Szyperski

    http://dx.doi.org/10.1021/acs.jpcb.1c10750 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Pulavarti, S. V. S. R. K., Maguire, J. B., Yuen, S., Harrison, J. S., Griffin, J., Premkumar, L., Esposito, E. A., Makhatadze, G. I., Garcia, A. E., Weiss, T. M., Snell, E. H., Kuhlman, B., & …

  57. From Static Structures to Continuous Conformational Changes on the Energy Landscapes

    0.0 out of 5 stars 

    30 Jul 2020 | BioXFEL Publications | Contributor(s): Ghoncheh Mashayekhi, Ali Dashti, Peter Schwander, Abbas Ourmazd

    http://dx.doi.org/10.1017/s1431927620018723 journal-article Mashayekhi, G. et al., 2020. From Static Structures to Continuous Conformational Changes on the Energy Landscapes. Microscopy and Microanalysis, 26(S2), pp.1614–1615. Available at: http://dx.doi.org/10.1017/s1431927620018723. Ghoncheh …

  58. From Systems to Structure: Bridging Networks and Mechanism

    0.0 out of 5 stars 

    24 Jan 2013 | BioXFEL Publications | Contributor(s): James S. Fraser, John D. Gross, Nevan J. Krogan

    journal-article http://dx.doi.org/10.1016/j.molcel.2013.01.003 Fraser, J.S., Gross, J.D. & Krogan, N.J., 2013. From Systems to Structure: Bridging Networks and Mechanism. Molecular Cell, 49(2), pp.222–231. Available at: http://dx.doi.org/10.1016/j.molcel.2013.01.003. James S. Fraser and …

  59. Frontiers of free-electron laser science II

    0.0 out of 5 stars 

    06 Sep 2016 | BioXFEL Publications | Contributor(s): Roger Falcone, Michael Dunne, Henry Chapman, Makina Yabashi, Kiyoshi Ueda

    http://dx.doi.org/10.1088/0953-4075/49/18/180201 journal-article Falcone, R. et al., 2016. Frontiers of free-electron laser science II. Journal of Physics B: Atomic, Molecular and Optical Physics, 49(18), p.180201. Available at: http://dx.doi.org/10.1088/0953-4075/49/18/180201. Roger Falcone and …

  60. Full inactivation of alphaviruses in single particle and crystallized forms

    0.0 out of 5 stars 

    26 Jul 2016 | BioXFEL Publications | Contributor(s): Robert M Lawrence, James D Zook, Brenda Hogue

    http://dx.doi.org/10.1016/j.jviromet.2016.07.020 Robert M. Lawrence and James D. Zook and Brenda G. Hogue Lawrence, R.M., Zook, J.D. & Hogue, B.G., 2016. Full inactivation of alphaviruses in single particle and crystallized forms. Journal of Virological Methods, 236, pp.237–244. Available at: …

  61. Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways

    0.0 out of 5 stars 

    28 Jun 2016 | BioXFEL Publications | Contributor(s): Tyler D. Huber, Fengbin Wang, Shanteri Singh, Brooke R. Johnson, Jianjun Zhang, Manjula Sunkara, Steven G. Van Lanen, Andrew J. Morris, George Phillips, Jon S. Thorson

    http://dx.doi.org/10.1021/acschembio.6b00348 journal-article Huber, T.D. et al., 2016. Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways. ACS Chemical Biology, 11(9), pp.2484–2491. Available at: http://dx.doi.org/10.1021/acschembio.6b00348. Tyler D. Huber and …

  62. Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles

    0.0 out of 5 stars 

    16 Jun 2014 | BioXFEL Publications | Contributor(s): Jo E. Lomax, Christopher M. Bianchetti, Aram Chang, George Phillips, Brian G. Fox, Ronald T. Raines

    http://dx.doi.org/10.1016/j.jmb.2014.06.007 journal-article Lomax, J.E. et al., 2014. Functional Evolution of Ribonuclease Inhibitor: Insights from Birds and Reptiles. Journal of Molecular Biology, 426(17), pp.3041–3056. Available at: http://dx.doi.org/10.1016/j.jmb.2014.06.007. Jo E. Lomax …

  63. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering

    0.0 out of 5 stars 

    12 Feb 2021 | 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.2020.11.1003 journal-article Menon, C.S.K. et al., 2021. Functional Expansion of G-Protein-Coupled Receptor Shown by Time-Resolved X-Ray Scattering. Biophysical Journal, 120(3), p.132a. Available at: http://dx.doi.org/10.1016/j.bpj.2020.11.1003. C. Swathi K. Menon …

  64. Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots

    0.0 out of 5 stars 

    30 Mar 2018 | BioXFEL Publications | Contributor(s): Ali Dashti, Mrinal Shekhar, Danya Ben Hail, Ghoncheh Mashayekhi, Peter Schwander, Amedee Des Georges, Joachim Frank, Abhishek Singharoy, Abbas Ourmazd

    http://dx.doi.org/10.1101/291922 We present a new approach to determining the conformational changes associated with biological function, and demonstrate its capabilities in the context of experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca2+-channel involved in …

  65. Fundamentals of Crystal Growth

    0.0 out of 5 stars 

    14 Oct 2015 | Teaching Materials | Contributor(s): Edward Snell, Eaton E Lattman

    Dr. Ed Lattman discusses the foundations of crystallography and theoretical and practical considerations including X-ray radiation and production and crystallization nucleation, growth and optimization.

  66. Generalized Born Implicit Solvent Models for Biomolecules

    0.0 out of 5 stars 

    11 Mar 2019 | BioXFEL Publications | Contributor(s): Alexey V. Onufriev, David Case

    http://dx.doi.org/10.1146/annurev-biophys-052118-115325 It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the …

  67. Generic GPCR residue numbers – aligning topology maps while minding the gaps

    0.0 out of 5 stars 

    22 Dec 2014 | BioXFEL Publications | Contributor(s): Vignir Isberg, Chris De Graaf, Andrea Bortolato, Vadim Cherezov, Vsevolod Katritch, Fiona H. Marshall, Stefan Mordalski, Jean-Philippe Pin, Raymond C. Stevens, Gerrit Vriend, David E. Gloriam

    http://dx.doi.org/10.1016/j.tips.2014.11.001 Vignir Isberg and Chris de Graaf and Andrea Bortolato and Vadim Cherezov and Vsevolod Katritch and Fiona H. Marshall and Stefan Mordalski and Jean-Philippe Pin and Raymond C. Stevens and Gerrit Vriend and David E. Gloriam Isberg, V. et al., 2015. Generic …

  68. Genetic interaction mapping informs integrative structure determination of protein complexes

    0.0 out of 5 stars 

    10 Dec 2020 | BioXFEL Publications | Contributor(s): Hannes Braberg, Ignacia Echeverria, Stefan Bohn, Peter Cimermancic, Anthony Shiver, Richard Alexander, Jiewei Xu, Michael Shales, Raghuvar Dronamraju, Shuangying Jiang, Gajendradhar Dwivedi, Derek Bogdanoff, Kaitlin K. Chaung, Ruth Hüttenhain, Shuyi Wang, David Mavor, Riccardo Pellarin, Dina Schneidman, Joel S. Bader, James Fraser, John Morris, James E. Haber, Brian D. Strahl, Carol A. Gross, Junbiao Dai, Jef D. Boeke, Andrej Sali, Nevan J. Krogan

    http://dx.doi.org/10.1126/science.aaz4910 Determining structures of protein complexes is crucial for understanding cellular functions. Here, we describe an integrative structure determination approach that relies on in vivo measurements of genetic interactions. We construct phenotypic profiles for …

  69. Genomic basis for the convergent evolution of electric organs

    0.0 out of 5 stars 

    26 Jun 2014 | BioXFEL Publications | Contributor(s): J. R. Gallant, L. L. Traeger, J. D. Volkening, H. Moffett, P.-H. Chen, C. D. Novina, G. N. Phillips, R. Anand, G. B. Wells, M. Pinch, R. Guth, G. A. Unguez, J. S. Albert, H. H. Zakon, M. P. Samanta, M. R. Sussman

    http://dx.doi.org/10.1126/science.1254432 journal-article Gallant, J.R. et al., 2014. Genomic basis for the convergent evolution of electric organs. Science, 344(6191), pp.1522–1525. Available at: http://dx.doi.org/10.1126/science.1254432. J. R. Gallant and L. L. Traeger and J. D. Volkening …

  70. Ghost imaging with x rays

    0.0 out of 5 stars 

    07 Sep 2016 | BioXFEL Publications | Contributor(s): Dilano Saldin

    journal-article http://dx.doi.org/10.1103/physics.9.103 Saldin, D., 2016. Ghost imaging with x rays. Physics, 9. Available at: http://dx.doi.org/10.1103/physics.9.103. Dilano Saldin

  71. Goniometer-based femtosecond crystallography with X-ray free electron lasers

    0.0 out of 5 stars 

    01 Nov 2014 | BioXFEL Publications | Contributor(s): Aina E. Cohen, S. Michael Soltis, Ana González, Laura Aguila, Roberto Alonso-Mori, Christopher Barnes, Elizabeth L. Baxter, Winnie Brehmer, Aaron S. Brewster, Axel T. Brunger, Guillermo Calero, Joseph F. Chang, Matthieu Chollet, Paul Ehrensberger, Thomas L. Eriksson, Yiping Feng, Johan Hattne, Britt Hedman, Michael Hollenbeck, James Holton, Stephen Keable, Brian K. Kobilka, Elena G. Kovaleva, Andrew C. Kruse, Henrik T. Lemke, Guowu Lin, Artem Y. Lyubimov, Aashish Manglik, Irimpan I. Mathews, Scott E. McPhillips, Silke Nelson, John W. Peters, Nicholas K. Sauter, Clyde A. Smith, Jinhu Song, Hilary P. Stevenson, Yingssu Tsai, Monarin Uervirojnangkoorn, Vladimir Vinetsky, Soichi Wakatsuki, William I. Weis, Oleg A. Zadvornyy, Oliver B. Zeldin, Diling Zhu, Keith O. Hodgson

    journal-article http://dx.doi.org/10.1073/pnas.1418733111 Cohen, A.E. et al., 2014. Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proceedings of the National Academy of Sciences, 111(48), pp.17122–17127. Available at: http://dx.doi.org/10.1073/pnas.1418733111. …

  72. GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine Receptor

    0.0 out of 5 stars 

    17 Aug 2022 | BioXFEL Publications | Contributor(s): Anna Shiriaeva, Daejin Park, Gyudong Kim, Yoonji Lee, Xiyan Hou, Dnyandev B. Jarhad, Gibae Kim, Jinha Yu, Young Eum Hyun, Woomi Kim, Zhan-Guo Gao, Kenneth A. Jacobson, Gye Won Han, Raymond C. Stevens, Lak Shin Jeong, Sun Choi, Vadim Cherezov

    http://dx.doi.org/10.1021/acs.jmedchem.2c00462 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Shiriaeva, A., Park, D., Kim, G., Lee, Y., Hou, X., Jarhad, D. B., Kim, G., Yu, J., Hyun, Y. E., Kim, W., Gao, Z.-G., Jacobson, K. A., Han, G. W., Stevens, R. C., Jeong, L. S., Choi, S., …

  73. GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1–2 September 2014

    0.0 out of 5 stars 

    13 Mar 2015 | BioXFEL Publications | Contributor(s): Alexander Heifetz, Gebhard F.X. Schertler, Roland Seifert, Christopher G. Tate, Patrick M. Sexton, Vsevolod V. Gurevich, Daniel Fourmy, Vadim Cherezov, Fiona H. Marshall, R. Ian Storer, Isabel Moraes, Irina G. Tikhonova, Christofer S. Tautermann, Peter Hunt, Tom Ceska, Simon Hodgson, Mike J. Bodkin, Shweta Singh, Richard J. Law, Philip C. Biggin

    http://dx.doi.org/10.1007/s00210-015-1111-8 Alexander Heifetz and Gebhard F. X. Schertler and Roland Seifert and Christopher G. Tate and Patrick M. Sexton and Vsevolod V. Gurevich and Daniel Fourmy and Vadim Cherezov and Fiona H. Marshall and R. Ian Storer and Isabel Moraes and Irina G. Tikhonova …

  74. Handling sample heterogeneity in serial crystallography

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    Oliver Zeldin (Stanford) Serial crystallography data is made up of images obtained from a population of slightly in-homogenous crystals. We will discuss clustering and filtering approaches to (1) characterizing sample heterogeneity in unmerged data, and (2) identifying optimal sub-sets of images …

  75. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase

    0.0 out of 5 stars 

    15 Oct 2020 | BioXFEL Publications | Contributor(s): Ming-Yue Lee, James Geiger, Andrii Ishchenko, Gye Won Han, Anton Barty, Thomas A. White, Cornelius Gati, Alexander Batyuk, Mark S. Hunter, Andrew Aquila, Sébastien Boutet, Uwe Weierstall, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.1107/s2052252520012701 Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has …

  76. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam

    0.0 out of 5 stars 

    07 Sep 2023 | BioXFEL Publications | Contributor(s): Tek Narsingh Malla, Kara Zielinski, Luis Aldama, Sasa Bajt, Denisse Feliz, Brendon Hayes, Mark S. Hunter, Christopher Kupitz, Stella Lisova, Juraj Knoska, Jose Manuel Martin-Garcia, Valerio Mariani, Suraj Pandey, Ishwor Poudyal, Raymond G. Sierra, Alexandra Tolstikova, Oleksandr Yefanov, Chung Hong Yoon, Abbas Ourmazd, Petra Fromme, Peter Schwander, Anton Barty, Henry Chapman, Emina Stojkovic, Alexander Batyuk, Sébastien Boutet, George Phillips, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1038/s41467-023-41246-1 AbstractFor decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free …

  77. High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide

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    15 Oct 2020 | BioXFEL Publications | Contributor(s): D Koulentianos, A E A Fouda, S H Southworth, J D Bozek, J Küpper, R Santra, N V Kryzhevoi, L S Cederbaum, C Bostedt, M Messerschmidt, N Berrah, L Fang, B Murphy, T Osipov, J P Cryan, J Glownia, S Ghimire, P J Ho, B Krässig, D Ray, Y Li, E P Kanter, L Young, G Doumy

    http://dx.doi.org/10.1088/1361-6455/abc183 journal-article Koulentianos, D. et al., 2020. High intensity x-ray interaction with a model bio-molecule system: double-core-hole states and fragmentation of formamide. Journal of Physics B: Atomic, Molecular and Optical Physics, 53(24), p.244005. …

  78. High numerical aperture multilayer Laue lenses

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    01 Jun 2015 | BioXFEL Publications | Contributor(s): Andrew J. Morgan, Mauro Prasciolu, Andrzej Andrejczuk, Jacek Krzywinski, Alke Meents, David Pennicard, Heinz Graafsma, Anton Barty, Richard J. Bean, Miriam Barthelmess, Dominik Oberthuer, Oleksandr Yefanov, Andrew Aquila, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1038/srep09892 Andrew J. Morgan and Mauro Prasciolu and Andrzej Andrejczuk and Jacek Krzywinski and Alke Meents and David Pennicard and Heinz Graafsma and Anton Barty and Richard J. Bean and Miriam Barthelmess and Dominik Oberthuer and Oleksandr Yefanov and Andrew Aquila and …

  79. High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter

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    20 Mar 2015 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Shatabdi Roy-Chowdhury, Jesse David Coe, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.5b00589 Bahige G. Abdallah and Shatabdi Roy-Chowdhury and Jesse Coe and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2015. High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter. Anal. Chem., 87(8), pp.4159–4167. Available at: …

  80. High-density grids for efficient data collection from multiple crystals

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    03 Dec 2015 | BioXFEL Publications | Contributor(s): Elizabeth L. Baxter, Laura Aguila, Roberto Alonso-Mori, Christopher Barnes, Christopher A. Bonagura, Winnie Brehmer, Axel T. Brunger, Guillermo Calero, Tom T. Caradoc-Davies, Ruchira Chatterjee, William F. Degrado, James Fraser, Mohamed Ibrahim, Jan Kern, Brian K. Kobilka, Andrew C. Kruse, Karl M. Larsson, Heinrik T. Lemke, Artem Y. Lyubimov, Aashish Manglik, Scott E. McPhillips, Erik Norgren, Siew S. Pang, S. M. Soltis, Jinhu Song, Jessica Thomaston, Yingssu Tsai, William I. Weis, Rahel Woldeyes, Vittal Yachandra, Junko Yano, Athina Zouni, Aina E. Cohen

    Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive …

  81. High-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle

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    17 Sep 2020 | BioXFEL Publications | Contributor(s): Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michal Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1101/2020.09.16.298463 AbstractPhytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting (dark) Pr state and the light activated Pfr state, in …

  82. High-resolution crystal structures of transient intermediates in the phytochrome photocycle

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    23 Mar 2021 | BioXFEL Publications | Contributor(s): Melissa Carrillo, Suraj Pandey, Juan Sanchez, Moraima Noda, Ishwor Poudyal, Luis Aldama, Tek Narsingh Malla, Elin Claesson, Weixiao Yuan Wahlgren, Denisse Feliz, Vukica Šrajer, Michał Maj, Leticia Castillon, So Iwata, Eriko Nango, Rie Tanaka, Tomoyuki Tanaka, Luo Fangjia, Kensuke Tono, Shigeki Owada, Sebastian Westenhoff, Emina Stojkovic, Marius Schmidt

    http://dx.doi.org/10.1016/j.str.2021.03.004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Carrillo, M. et al., 2021. High-resolution crystal structures of transient intermediates in the phytochrome photocycle. Structure. Available at: http://dx.doi.org/10.1016/j.str.2021.03.004. …

  83. High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

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    29 Oct 2013 | BioXFEL Publications | Contributor(s): James D Zook, Trivikram R. Molugu, Neil E. Jacobsen, Guangxin Lin, Jürgen Soll, Brian R. Cherry, Michael F. Brown, Petra Fromme

    http://dx.doi.org/10.1371/journal.pone.0078116 journal-article Zook, J.D. et al., 2013. High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane O. Y. Dmitriev, ed. PLoS ONE, 8(10), p.e78116. Available at: …

  84. High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3

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    18 Apr 2015 | BioXFEL Publications | Contributor(s): James D Zook, Nicholas Sisco, Gina Mo, Debra Hansen, Felicia Craciunescu, Brian Cherry, Kathryn Sykes, Wade Van Horn, Petra Fromme

    http://dx.doi.org/10.1016/j.bpj.2013.11.1142 journal-article Zook, J.D. et al., 2014. High-Resolution NMR Spectroscopy Reveals Structure of Lipoprotein flpp3. Biophysical Journal, 106(2), p.193a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.1142. James D. Zook and Nicholas Sisco and …

  85. High-resolution structure of viruses from random diffraction snapshots

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): A. Hosseinizadeh, P. Schwander, A. Dashti, R. Fung, R. M. D'Souza, A. Ourmazd

    http://dx.doi.org/10.1098/rstb.2013.0326 A. Hosseinizadeh and P. Schwander and A. Dashti and R. Fung and R. M. D'Souza and A. Ourmazd Hosseinizadeh, A. et al., 2014. High-resolution structure of viruses from random diffraction snapshots. Philosophical Transactions of the Royal Society B: …

  86. High-resolution structure of viruses from random diffraction snapshots

    0.0 out of 5 stars 

    13 Oct 2015 | Teaching Materials

    The advent of the X-ray free-electron laser (XFEL) has made it possible to record diffraction snapshots of biological entities injected into the X-ray beam before the onset of radiation damage. Algorithmic means must then be used to determine the snapshot orientations and thence the …

  87. High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

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    02 Nov 2015 | BioXFEL Publications | Contributor(s): Jessica L. Thomaston, Mercedes Alfonso-Prieto, Rahel Woldeyes, James Fraser, Michael L. Klein, Giacomo Fiorin, William F. DeGrado

    http://dx.doi.org/10.1073/pnas.1518493112 Jessica L. Thomaston and Mercedes Alfonso-Prieto and Rahel A. Woldeyes and James S. Fraser and Michael L. Klein and Giacomo Fiorin and William F. DeGrado Thomaston, J.L. et al., 2015. High-resolution structures of the M2 channel from influenza A virus …

  88. High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions

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    04 Jan 2018 | BioXFEL Publications | Contributor(s): Jana Broecker, Takefumi Morizumi, Wei-Lin Ou, Viviane Klingel, Anling Kuo, David J Kissick, Andrii Ishchenko, Ming-Yue Lee, Shenglan Xu, Oleg Makarov, Vadim Cherezov, Craig M Ogata, Oliver P Ernst

    http://dx.doi.org/10.1038/nprot.2017.135 journal-article Broecker, J. et al., 2018. High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Nature Protocols, 13(2), pp.260–292. Available at: …

  89. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application

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    03 Dec 2019 | BioXFEL Publications | Contributor(s): Geoffrey W. Grime, Oliver B. Zeldin, Mary E. Snell, Edward D. Lowe, John F. Hunt, Gaetano T. Montelione, Liang Tong, Edward Snell, Elspeth F. Garman

    http://dx.doi.org/10.1021/jacs.9b09186 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Grime, G.W. et al., 2019. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. Journal of the American Chemical …

  90. High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source

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    04 Apr 2019 | BioXFEL Publications | Contributor(s): Jose M. Martin-Garcia, Lan Zhu, Derek Mendez, Ming-Yue Lee, Eugene Chun, Chufeng Li, Hao Hu, GANESH SUBRAMANIAN, David Kissick, Craig Ogata, Robert Henning, Andrii Ishchenko, Zachary Dobson, Shangji Zhang, Uwe Weierstall, John Spence, Petra Fromme, Nadia Zatsepin, Robert F. Fischetti, Vadim Cherezov, Wei Liu

    http://dx.doi.org/10.1107/s205225251900263x Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron …

  91. Hit Rate Calculator

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    01 Apr 2015 | Downloads | Contributor(s): Tom Grant

    Data Analysis Scripts 'hits' is a python script that can be used to quickly calculate hits and hit rates from a series of different experimental runs from an SFX experiment when using Cheetah for hit finding. It uses Cheetah's frames.txt file to calculate hits.  By default it will use your own …

  92. Hollow cone illumination for fast TEM, and outrunning damage with electrons

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    23 Sep 2015 | BioXFEL Publications | Contributor(s): J C H Spence, G Subramanian, P Musumeci

    http://dx.doi.org/10.1088/0953-4075/48/21/214003 J C H Spence and G Subramanian and P Musumeci Spence, J.C.H., Subramanian, G. & Musumeci, P., 2015. Hollow cone illumination for fast TEM, and outrunning damage with electrons. Journal of Physics B: Atomic, Molecular and Optical Physics, 48(21), …

  93. How 2'- O -Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation

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    06 Feb 2018 | BioXFEL Publications | Contributor(s): Junhong Choi, Gabriele Indrisiunaite, Hasan Demirci, Ka-Weng Ieong, Jinfan Wang, Alexey Petrov, Arjun Prabhakar, Gideon Rechavi, Dan Dominissini, Chuan He, Måns Ehrenberg, Joseph D. Puglisi

    http://dx.doi.org/10.1016/j.bpj.2017.11.3237 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Choi, J. et al., 2018. How 2’- O -Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation. Biophysical Journal, 114(3), p.592a. Available at: …

  94. How Cubic Can Ice Be?

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    28 Jun 2017 | BioXFEL Publications | Contributor(s): Andrew J. Amaya, Harshad Pathak, Viraj P. Modak, Hartawan Laksmono, N. Duane Loh, Jonas A. Sellberg, Raymond G. Sierra, Trevor A. McQueen, Matt J. Hayes, Garth J. Williams, Marc Messerschmidt, Sébastien Boutet, Michael J. Bogan, Anders Nilsson, Claudiu A. Stan, Barbara E. Wyslouzil

    http://dx.doi.org/10.1021/acs.jpclett.7b01142 journal-article Amaya, A.J. et al., 2017. How Cubic Can Ice Be? The Journal of Physical Chemistry Letters, pp.3216–3222. Available at: http://dx.doi.org/10.1021/acs.jpclett.7b01142. Andrew J. Amaya and Harshad Pathak and Viraj P. Modak and Hartawan …

  95. How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

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    19 Nov 2020 | BioXFEL Publications | Contributor(s): Renee Otten, Ricardo A. P. Pádua, H. Adrian Bunzel, Vy Nguyen, Warintra Pitsawong, MacKenzie Patterson, Shuo Sui, Sarah Perry, Aina E. Cohen, Donald Hilvert, Dorothee Kern

    http://dx.doi.org/10.1126/science.abd3623 The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of NMR, crystallographic, and stopped-flow techniques to an …

  96. How good are my data?

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    29 Aug 2014 | Teaching Materials

    Nick Sauter (LBNL) A design goal of the data reduction package cctbx.xfel is to discover and apply the numerous systematic corrections necessary to correctly model XFEL diffraction images. Numerous challenges must be addressed to interpret serial femtosecond diffraction, including an inaccurate …

  97. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain

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    04 Oct 2018 | BioXFEL Publications | Contributor(s): Yen-Lin Chen, Julie L. Sutton, Lois Pollack

    http://dx.doi.org/10.1021/acs.jpcb.8b07262 journal-article Chen, Y.-L., Sutton, J.L. & Pollack, L., 2018. How the Conformations of an Internal Junction Contribute to Fold an RNA Domain. The Journal of Physical Chemistry B. Available at: http://dx.doi.org/10.1021/acs.jpcb.8b07262. Yen-Lin Chen …

  98. ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding

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    06 Nov 2006 | BioXFEL Publications | Contributor(s): H. Chapman, C. Tang, L. Robillard, Y. Kim, Y. Wei

    http://dx.doi.org/10.1111/j.1538-7836.2006.00294.x journal-article Chapman, H. et al., 2006. ID: 294 Tumor Cell Signaling Through Integrin alpha5beta1 Requires Urokinase Receptor Binding. Journal of Thrombosis and Haemostasis, 4(s1), pp.78–78. Available at: …

  99. Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies

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    12 Oct 2022 | BioXFEL Publications | Contributor(s): Halilibrahim Ciftci, Belgin Sever, Esra Ayan, Mustafa Can, Hasan Demirci, Masami Otsuka, Amaç Fatih TuYuN, Hiroshi Tateishi, Mikako Fujita

    http://dx.doi.org/10.3390/ph15101255 The HIV-1 Gag protein binds to the host cell membrane and assembles into immature particles. Then, in the course of immature virion budding, activated protease cleaves Gag into its main components: MA, CA, NC, and p6 proteins. The highly basic residues of MA …

  100. Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors

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    27 Jul 2017 | BioXFEL Publications | Contributor(s): X. Edward Zhou, Yuanzheng He, Parker W. De Waal, Xiang Gao, Yanyong Kang, Ned Van Eps, Yanting Yin, Kuntal Pal, Devrishi Goswami, Thomas A. White, Anton Barty, Naomi R. Latorraca, Henry Chapman, Wayne L. Hubbell, Ron O. Dror, Raymond C. Stevens, Vadim Cherezov, Vsevolod V. Gurevich, Patrick R. Griffin, Oliver P. Ernst, Karsten Melcher, H. Eric Xu

    http://dx.doi.org/10.1016/j.cell.2017.07.002 journal-article Zhou, X.E. et al., 2017. Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors. Cell, 170(3), pp.457–469.e13. Available at: http://dx.doi.org/10.1016/j.cell.2017.07.002. X. Edward Zhou and …