Resources: All

Submit a resource

Finding a resource

Use the sorting or filtering options to sort results and/or narrow down the list of resources.

Use the 'Search' to find specific resources by title or description.

Popular Tags

  1. animals
  2. chemistry
  3. crystallography
  4. Data Analysis
  5. diffraction
  6. electrons
  7. instrumentation
  8. lasers
  9. LCLS
  10. methods
  11. models
  12. molecular
  13. muramidase
  14. protein conformation
  15. proteins
  16. radiation effects
  17. scattering
  18. time factors
  19. x-ray
  20. x-ray diffraction

Click a tag to see only resources with that tag.

Search for Courses

  1. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free Electron Laser

    0.0 out of 5 stars 

    18 Apr 2015 | BioXFEL Publications | Contributor(s): Jesse David Coe, Christopher Kupitz, Shibom Basu, Chelsie E Conrad, Shatabdi Roy-Chowdhury, Raimund Fromme, Petra Fromme

    http://dx.doi.org/10.1016/bs.mie.2015.01.011 Jesse Coe and Christopher Kupitz and Shibom Basu and Chelsie E. Conrad and Shatabdi Roy-Chowdhury and Raimund Fromme and Petra Fromme Coe, J. et al., 2015. Crystallization of Photosystem II for Time-Resolved Structural Studies Using an X-ray Free …

  2. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    0.0 out of 5 stars 

    05 Nov 2013 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Christopher Kupitz, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/nn402515q Bahige G. Abdallah and Christopher Kupitz and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2013. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel. ACS Nano, 7(12), pp.10534–10543. Available at: …

  3. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    0.0 out of 5 stars 

    09 Oct 2015 | Teaching Materials

    Traditional macroscale protein crystallization is accomplished nontrivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time-consuming and resource-intensive, hindering protein structure determination. Even …

  4. Crystallization screening: the influence of history on current practice

    0.0 out of 5 stars 

    26 Jun 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Janet Newman, Edward Snell

    While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. …

  5. Crystallographic data processing for free-electron laser sources

    0.0 out of 5 stars 

    14 Jun 2013 | BioXFEL Publications | Contributor(s): Thomas A. White, Anton Barty, Francesco Stellato, James Holton, Richard Kirian, Nadia Zatsepin, Henry Chapman

    A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suiteCrystFELand the pre-processing programCheetah. A detailed analysis of the nature and impact of …

  6. Crystallographic Methods - Crystallographic Symmetry - Part I

    0.0 out of 5 stars 

    20 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  7. Crystallographic Methods - Crystallographic Symmetry - Part II

    0.0 out of 5 stars 

    20 Oct 2014 | Teaching Materials

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  8. Crystallographic Methods - Crystallographic Symmetry - Part III

    0.0 out of 5 stars 

    22 Oct 2014 | Teaching Materials | Contributor(s): Edward Snell

    Dr. Edward Snell Diffraction measurements     Crystal classes and Laue groups; Diffraction symmetry – Friedel and Bijvoet pairs; Space group determination – Systematic extinctions; Reading the International Tables; Non-crystallographic symmetry Rupp, chs. 8, 6 (§6.5), and 5 (§5.2)

  9. Crystallographic Methods - Geometrical Crystallography - Part I

    0.0 out of 5 stars 

    19 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  10. Crystallographic Methods - Geometrical Crystallography - Part II

    0.0 out of 5 stars 

    04 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Geometrical crystallography     Laws of classical crystallography; Lattices, point groups, space groups; Crystal faces, lattice planes, and Miller indices; The Bragg equation and the Ewald construction; Reciprocal space and the reciprocal lattice Rupp, ch. 5

  11. Crystallographic Methods - Introduction and Overview

    0.0 out of 5 stars 

    25 Aug 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing Introduction     Protein structural elements: 1° aa sequence,  2° α-helix, β strand, β sheet, loop, 3° domain fold,  4° domain assembly; Overview of biomacromolecular crystallography

  12. Crystallographic Methods - X-ray Diffraction Physics - Part I

    0.0 out of 5 stars 

    08 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  13. Crystallographic Methods - X-ray Diffraction Physics - Part II

    0.0 out of 5 stars 

    11 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  14. Crystallographic Methods - X-ray Diffraction Physics - Part III

    0.0 out of 5 stars 

    15 Sep 2014 | Teaching Materials

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  15. Crystallographic Methods - X-ray Diffraction Physics - Part IV

    0.0 out of 5 stars 

    18 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  16. Crystallographic Methods - X-ray Diffraction Physics - Part IX

    0.0 out of 5 stars 

    03 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  17. Crystallographic Methods - X-ray Diffraction Physics - Part V

    0.0 out of 5 stars 

    22 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  18. Crystallographic Methods - X-ray Diffraction Physics - Part VI

    0.0 out of 5 stars 

    25 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  19. Crystallographic Methods - X-ray Diffraction Physics - Part VII

    0.0 out of 5 stars 

    28 Sep 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  20. Crystallographic Methods - X-ray Diffraction Physics - Part VIII

    0.0 out of 5 stars 

    01 Oct 2014 | Teaching Materials | Contributor(s): Robert H Blessing

    Dr. Bob Blessing X-Ray diffraction physics     X-Ray sources; Wave nature of X-rays; X-Ray scattering by an electron, an atom, a molecule, by a lattice row, a lattice plane, by a crystal – Laue diffraction / Bragg reflection; The crystal structure factor Rupp, ch. 6

  21. Crystallographic Methods of Structural Biology

    0.0 out of 5 stars 

    18 Sep 2016 | Courses | Contributor(s): Robert H Blessing, Edward Snell

    The goal of the course is that students acquire sufficient knowledge and understanding of the basic principles of biomolecular crystal structure analysis that they will be able to comfortably, and with interest and insight, read and comprehend the articles in Volume F of the International Tables …

  22. Crystallography with an XFEL

    0.0 out of 5 stars 

    21 Jul 2015 | Seminars | Contributor(s): Marc Messerschmidt

    Dr. Marc Messerschmidt discusses the design and operation of the X-ray free electron laser at the LCLS. Be sure to grab the attached MP3 audio file to follow along. Topics discussed include: - XFEL fundamentals - LCLS machine capabilities and energy spectrum - Beamlines and instrumentation for …

  23. Crystallography: Sources of inspiration

    0.0 out of 5 stars 

    28 Jan 2014 | BioXFEL Publications | Contributor(s): Sean McSweeney, Petra Fromme

    http://dx.doi.org/10.1038/505620a Sean McSweeney and Petra Fromme McSweeney, S. & Fromme, P., 2014. Crystallography: Sources of inspiration. Nature, 505(7485), pp.620–621. Available at: http://dx.doi.org/10.1038/505620a. journal-article

  24. CrystFEL Tutorial

    0.0 out of 5 stars 

    03 Sep 2014 | Teaching Materials

    Tom White (CFEL)

  25. Curiosity: a tool for exploring density features in crystallographic and cryoEM maps

    0.0 out of 5 stars 

    11 Feb 2022 | BioXFEL Publications | Contributor(s): Iris Diane Young, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.11.2781 journal-article Young, I. D., & Fraser, J. S. (2022). Curiosity: a tool for exploring density features in crystallographic and cryoEM maps. Biophysical Journal, 121(3), 528a. https://doi.org/10.1016/j.bpj.2021.11.2781 Iris D. Young and James S. Fraser

  26. Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis: Supplemental Information

    0.0 out of 5 stars 

    19 Jan 2019 | BioXFEL Publications | Contributor(s): Medhanjali DasGupta, Dominik Budday, Peter Madzelan, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Roberto Alonso-Mori, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra Tiwari, David B. Berkowitz, Michael Thompson, James Fraser, Michael E. Wall, Henry Van Den Bedem, Mark A. Wilson

    http://dx.doi.org/10.1101/524751 Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site …

  27. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization

    0.0 out of 5 stars 

    30 Jan 2017 | BioXFEL Publications | Contributor(s): Madison B. Adolph, Anjuman Ara, Yuqing Feng, Cristina J. Wittkopp, Michael Emerman, James Fraser, Linda Chelico

    journal-article http://dx.doi.org/10.1093/nar/gkx066 Adolph, M.B. et al., 2017. Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucleic Acids Research, 45(6), pp.3378–3394. Available at: http://dx.doi.org/10.1093/nar/gkx066. …

  28. Damage threshold of amorphous carbon mirror for 177eV FEL radiation

    0.0 out of 5 stars 

    10 Nov 2010 | BioXFEL Publications | Contributor(s): Sh. Dastjani Farahani, Jaromir Chalupsky, T. Burian, Henry Chapman, A.J. Gleeson, V. Hajkoya, L. Juha, M. Jurek, Dorota Klinger, Harald Sinn, R. Sobierajski, M. Störmer, K. Tiedtke, S. Toleikis, Thomas Tschentscher, H. Wabnitz, Jerome Gaudin

    http://dx.doi.org/10.1016/j.nima.2010.10.133 journal-article Dastjani Farahani, S. et al., 2011. Damage threshold of amorphous carbon mirror for 177eV FEL radiation. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, …

  29. Dan Salah Tawfik (1955‐2021)—A giant of protein evolution

    0.0 out of 5 stars 

    28 May 2021 | BioXFEL Publications | Contributor(s): Mikael H Elias, James Fraser, Shina Caroline Lynn Kamerlin, Wayne M Patrick, Colin J Jackson

    http://dx.doi.org/10.15252/embr.202153256 journal-article Elias, M.H. et al., 2021. Dan Salah Tawfik (1955‐2021)—A giant of protein evolution. EMBO reports. Available at: http://dx.doi.org/10.15252/embr.202153256. Mikael H Elias and James S Fraser and Shina Caroline Lynn Kamerlin and Wayne M …

  30. Data Analysis and Sample Delivery

    0.0 out of 5 stars 

    29 Aug 2014 | Teaching Materials

    John Spence (ASU/LBNL) How XFEL MX differs from MX and why we do it.

  31. Data Analysis Scripts

    5.0 out of 5 stars 

    21 Jul 2015 | Downloads

    A repository of useful scripts for the analysis of XFEL data. 

  32. Data assimilation in operator algebras

    0.0 out of 5 stars 

    17 Feb 2023 | BioXFEL Publications | Contributor(s): David Freeman, Dimitrios Giannakis, Brian Mintz, Abbas Ourmazd, Joanna Slawinska

    http://dx.doi.org/10.1073/pnas.2211115120 We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by …

  33. Data publication with the structural biology data grid supports live analysis

    0.0 out of 5 stars 

    07 Mar 2016 | BioXFEL Publications | Contributor(s): Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Adrian R. Ferré-D'Amaré, J. Christopher Fromme, K. Christopher Garcia, Rachelle Gaudet, Peng Gong, Stephen C. Harrison, Ekaterina E. Heldwein, Zongchao Jia, Robert J. Keenan, Andrew C. Kruse, Marc Kvansakul, Jason S. McLellan, Yorgo Modis, Yunsun Nam, Zbyszek Otwinowski, Emil F. Pai, Pedro José Barbosa Pereira, Carlo Petosa, C. S. Raman, Tom A. Rapoport, Antonina Roll-Mecak, Michael K. Rosen, Gabby Rudenko, Joseph Schlessinger, Thomas U. Schwartz, Yousif Shamoo, Holger Sondermann, Yizhi J. Tao, Niraj H. Tolia, Oleg V. Tsodikov, Kenneth D. Westover, Hao Wu, Ian Foster, James Fraser, Filipe R. N C. Maia, Tamir Gonen, Tom Kirchhausen, Kay Diederichs, Mercè Crosas, Piotr Sliz

    journal-article http://dx.doi.org/10.1038/ncomms10882 Meyer, P.A. et al., 2016. Data publication with the structural biology data grid supports live analysis. Nature Communications, 7, p.10882. Available at: http://dx.doi.org/10.1038/ncomms10882. Peter A. Meyer and Stephanie Socias and Jason Key …

  34. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure

    0.0 out of 5 stars 

    27 Sep 2016 | BioXFEL Publications | Contributor(s): Jacques-Philippe Colletier, Michael R. Sawaya, Mari Gingery, Jose A. Rodriguez, Duilio Cascio, Aaron S. Brewster, Tara Michels-Clark, Robert H. Hice, Nicolas Coquelle, Sébastien Boutet, Garth J. Williams, Marc Messerschmidt, Daniel P. DePonte, Raymond G. Sierra, Hartawan Laksmono, Jason E. Koglin, Mark S. Hunter, Hyun-Woo Park, Monarin Uervirojnangkoorn, Dennis K. Bideshi, Axel T. Brunger, Brian A. Federici, Nicholas K. Sauter, David S. Eisenberg

    http://dx.doi.org/10.1038/nature19825 Jacques-Philippe Colletier and Michael R. Sawaya and Mari Gingery and Jose A. Rodriguez and Duilio Cascio and Aaron S. Brewster and Tara Michels-Clark and Robert H. Hice and Nicolas Coquelle and Sébastien Boutet and Garth J. Williams and Marc Messerschmidt and …

  35. De novo protein crystal structure determination from X-ray free-electron laser data

    0.0 out of 5 stars 

    22 Nov 2013 | BioXFEL Publications | Contributor(s): Thomas R. M. Barends, Lutz Foucar, Sabine Botha, R. Bruce Doak, Robert L. Shoeman, Karol Nass, Jason E. Koglin, Garth J. Williams, Sébastien Boutet, Marc Messerschmidt, Ilme Schlichting

    http://dx.doi.org/10.1038/nature12773 journal-article Barends, T.R.M. et al., 2013. De novo protein crystal structure determination from X-ray free-electron laser data. Nature, 505(7482), pp.244–247. Available at: http://dx.doi.org/10.1038/nature12773. Thomas R. M. Barends and Lutz Foucar and …

  36. De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography

    0.0 out of 5 stars 

    08 Aug 2018 | BioXFEL Publications | Contributor(s): S. Botha, D. Baitan, K. E. J. Jungnickel, D. Oberthür, C. Schmidt, S. Stern, M. O. Wiedorn, M. Perbandt, H. N. Chapman, C. Betzel

    http://dx.doi.org/10.1107/s2052252518009223 During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application …

  37. Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning

    0.0 out of 5 stars 

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

    http://dx.doi.org/10.1107/s0108767321098731 journal-article Chen, Y.-L., & Pollack, L. (2021). Decoding hidden structural information in solution wide-angle X-ray scattering (WAXS): from ensemble modeling to machine learning. Acta Crystallographica Section A Foundations and Advances, 77(a1), …

  38. Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases

    0.0 out of 5 stars 

    01 Mar 2024 | BioXFEL Publications | Contributor(s): Edwin G. Peña-Martínez, Jose Arcadio Rodriguez-Martinez

    http://dx.doi.org/10.31083/j.fbs1601004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E. G., & Rodríguez-Martínez, J. A. (2024). Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases. Frontiers in …

  39. Deconvoluting receptor trafficking, regulation, and function using massively parallel assays

    0.0 out of 5 stars 

    11 Feb 2022 | BioXFEL Publications | Contributor(s): David Nedrud, Yungui He, Daniel Schmidt, James Fraser, Willow Coyote-Maestas

    http://dx.doi.org/10.1016/j.bpj.2021.11.2700 journal-article Nedrud, D., He, Y., Schmidt, D., Fraser, J., & Coyote-Maestas, W. (2022). Deconvoluting receptor trafficking, regulation, and function using massively parallel assays. Biophysical Journal, 121(3), 2a. …

  40. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment

    0.0 out of 5 stars 

    09 Jun 2014 | BioXFEL Publications | Contributor(s): K. Pande, P. Schwander, M. Schmidt, D. K. Saldin

    http://dx.doi.org/10.1098/rstb.2013.0332 K. Pande and P. Schwander and M. Schmidt and D. K. Saldin Pande, K. et al., 2014. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment. Philosophical Transactions of the Royal Society B: …

  41. Deducing fast electron density changes in uncrystallized biomolecules

    0.0 out of 5 stars 

    13 Oct 2015 | Teaching Materials

    We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a …

  42. DefNEtTrp: An Iron Dual Chelator Approach for Anticancer Application

    0.0 out of 5 stars 

    04 Dec 2024 | BioXFEL Publications | Contributor(s): Israel Rodriguez, Carmen Acosta, Christopher Nieves-Escobar, Estelle Strangmark, Oscar Claudio-Ares, Adriana I. Vargas Figueroa, Alexandra M. Soto-Millán, Aixa M. Orta-Rivera, Andrei V. Astashkin, Arthur Tinoco

    https://doi.org/10.1021/jacsau.4c00774 journal-article Rodríguez, I., Acosta, C., Nieves-Escobar, C., Strangmark, E., Claudio-Ares, O., Vargas Figueroa, A. I., Soto-Millán, A. M., M. Orta-Rivera, A., Astashkin, A. V., & Tinoco, A. D. (2024). DefNEtTrp: An Iron Dual Chelator Approach for …

  43. Demonstration of simultaneous experiments using thin crystal multiplexing at the Linac Coherent Light Source

    0.0 out of 5 stars 

    09 Apr 2015 | BioXFEL Publications | Contributor(s): Y. Feng, R. Alonso-Mori, T. R. M. Barends, V. D. Blank, S. Botha, M. Chollet, D. S. Damiani, R. B. Doak, J. M. Glownia, J. M. Koglin, H. T. Lemke, M. Messerschmidt, K. Nass, S. Nelson, I. Schlichting, R. L. Shoeman, Yu. V. Shvyd'ko, M. Sikorski, S. Song, S. Stoupin, S. Terentyev, G. J. Williams, D. Zhu, A. Robert, S. Boutet

    Multiplexing of the Linac Coherent Light Source beam was demonstrated for hard X-rays by spectral division using a near-perfect diamond thin-crystal monochromator operating in the Bragg geometry. The wavefront and coherence properties of both the reflected and transmitted beams were well preserved, …

  44. DENSS: Ab Initio Electron Density Maps from Biological SAXS Data

    0.0 out of 5 stars 

    20 Mar 2019 | Seminars | Contributor(s): Thomas Grant

    Small angle scattering is an experimental technique used to analyze the molecular structures of a wide variety of biological and non-biological samples in solution. In contrast to X-ray crystallography and cryo-electron microscopy, where 3D electron density maps are calculated, available methods …

  45. Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography

    0.0 out of 5 stars 

    11 Sep 2023 | BioXFEL Publications | Contributor(s): Izumi Ishigami, Sergio Carbajo, Nadia Zatsepin, Masahide Hikita, Chelsie E Conrad, Garrett Charles Nelson, Jesse David Coe, Shibom Basu, Thomas Grant, Matthew H. Seaberg, Raymond G. Sierra, Mark S. Hunter, Petra Fromme, Raimund Fromme, Denis L. Rousseau, Syun-Ru Yeh

    http://dx.doi.org/10.1021/jacs.3c07803 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C. E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M. H., Sierra, R. G., Hunter, M. S., Fromme, P., Fromme, R., Rousseau, D. …

  46. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization

    0.0 out of 5 stars 

    18 Apr 2015 | BioXFEL Publications | Contributor(s): Katerina Dörner, Jose Martin Garcia, Christopher Kupitz, Rebekka M. Wachter, Petra Fromme

    http://dx.doi.org/10.1016/j.bpj.2013.11.2597 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Dörner, K. et al., 2014. Detection of Protein Nanocrystals Based on the Reversibility of Crystallization. Biophysical Journal, 106(2), p.458a. Available at: …

  47. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting

    0.0 out of 5 stars 

    26 Aug 2015 | BioXFEL Publications | Contributor(s): David Mavor, James Fraser, Ron Morganti

    http://dx.doi.org/10.1101/025452 Ubiquitination is an essential post-translational regulatory process that can control protein stability, localization, and activity. Ubiquitin is essential for eukaryotic life and is highly conserved, varying in only 3 amino acid positions between yeast and humans. …

  48. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

    0.0 out of 5 stars 

    25 Apr 2016 | BioXFEL Publications | Contributor(s): David Mavor, Kyle Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane Ó Conchúir, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, James Fraser

    Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced …

  49. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements

    0.0 out of 5 stars 

    16 Jun 2015 | BioXFEL Publications | Contributor(s): Steve P. Meisburger, Suzette A. Pabit, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2015.05.006 journal-article Meisburger, S.P., Pabit, S.A. & Pollack, L., 2015. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophysical Journal, 108(12), pp.2886–2895. Available at: …

  50. Determining the structural ensembles of disordered RNA and proteins using an integrated approach

    0.0 out of 5 stars 

    15 Sep 2022 | BioXFEL Publications | Contributor(s): Tong Wang, Suzette Pabit, Anja Henning-Knechtel, Weiwei He, Serdal Kirmizaltin, Lois Pollack

    http://dx.doi.org/10.1107/s205327332209831x journal-article Wang, T., Pabit, S., Henning-Knechtel, A., He, W., Kirmizaltin, S., & Pollack, L. (2022). Determining the structural ensembles of disordered RNA and proteins using an integrated approach. Acta Crystallographica Section A Foundations and …

  51. Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device

    0.0 out of 5 stars 

    05 May 2016 | BioXFEL Publications | Contributor(s): Jinghui Luo, Katherine A. Muratore, Edgar A. Arriaga, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.6b00837 Jinghui Luo and Katherine A. Muratore and Edgar A. Arriaga and Alexandra Ros Luo, J. et al., 2016. Deterministic Absolute Negative Mobility for Micro- and Submicrometer Particles Induced in a Microfluidic Device. Analytical Chemistry, 88(11), …

  52. Deterministic Ratchet for Sub-micrometer (Bio)particle Separation

    0.0 out of 5 stars 

    06 Mar 2018 | BioXFEL Publications | Contributor(s): Daihyun Kim, Jinghui Luo, Edgar A. Arriaga, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.7b03774 journal-article Kim, D. et al., 2018. Deterministic Ratchet for Sub-micrometer (Bio)particle Separation. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.7b03774. Daihyun Kim and Jinghui Luo and Edgar A. Arriaga and …

  53. Developing mix-and-inject serial crystallography at synchrotrons

    0.0 out of 5 stars 

    10 May 2024 | BioXFEL Publications | Contributor(s): K. A. Zielinski, L. Pollack

    https://doi.org/10.1107/s2053273323090666 journal-article Zielinski, K. A., & Pollack, L. (2023). Developing mix-and-inject serial crystallography at synchrotrons. Acta Crystallographica Section A Foundations and Advances, 79(a2), C550–C550. https://doi.org/10.1107/s2053273323090666 K. A. …

  54. Development of a ceramic injection molding process for liquid jet nozzles to be applied for X-ray free-electron lasers

    0.0 out of 5 stars 

    24 Jul 2017 | BioXFEL Publications | Contributor(s): Volker Piotter, Alexander Klein, Klaus Plewa, Kenneth R. Beyerlein, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1007/s00542-017-3493-7 journal-article Piotter, V. et al., 2017. Development of a ceramic injection molding process for liquid jet nozzles to be applied for X-ray free-electron lasers. Microsystem Technologies. Available at: http://dx.doi.org/10.1007/s00542-017-3493-7. …

  55. Development of a photophoretic optical guide for femtosecond x-ray diffractive imaging of aerosolized nanoparticles (Conference Presentation)

    0.0 out of 5 stars 

    10 Nov 2016 | BioXFEL Publications | Contributor(s): Richard Kirian, Salah Awel, Max Oliver Wiedorn, Daniel Horke, Nils Roth, Niko O. Eckerskorn, Jochen Küpper, Henry Chapman, Andrei V. Rode

    http://dx.doi.org/10.1117/12.2239171 Richard A. Kirian and Salah Awel and Max Wiedorn and Daniel Horke and Nils Roth and Niko O. Eckerskorn and Jochen Küpper and Henry N. Chapman and Andrei V. Rode Kirian, R.A. et al., 2016. Development of a photophoretic optical guide for femtosecond x-ray …

  56. Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source

    0.0 out of 5 stars 

    22 Mar 2013 | BioXFEL Publications | Contributor(s): D Shapiro, S Roy, R Celestre, W Chao, D Doering, M Howells, S Kevan, D Kilcoyne, J Kirz, S Marchesini, K A Seu, A Schirotzek, J Spence, T Tyliszczak, T Warwick, D Voronov, H A Padmore

    http://dx.doi.org/10.1088/1742-6596/425/19/192011 journal-article Shapiro, D. et al., 2013. Development of coherent scattering and diffractive imaging and the COSMIC facility at the Advanced Light Source. Journal of Physics: Conference Series, 425(19), p.192011. Available at: …

  57. Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future

    0.0 out of 5 stars 

    10 Aug 2018 | BioXFEL Publications | Contributor(s): Adrian P. Mancuso, Andrew Aquila, Richard Bean, Johan Bielecki, Carsten Fortmann-Grote, Klaus Giewekemeyer, Yoonhee Kim, Ruslan Kurta, Romain Letrun, Masoud Mehrjoo, Marc Messerschmidt, Grant Mills, Adam Round, Tokushi Sato, Joachim Schulz, Marcin Sikorski, Stephan Stern, Patrik Vagovic, Thomas Tschentscher

    http://dx.doi.org/10.1017/s143192761801276x journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Mancuso, A.P. et al., 2018. Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future. Microscopy and Microanalysis, 24(S2), pp.76–77. …

  58. Dielectrophoresis of lambda-DNA using 3D carbon electrodes

    0.0 out of 5 stars 

    24 Jan 2013 | BioXFEL Publications | Contributor(s): Rodrigo Martinez-Duarte, Fernanda Camacho-Alanis, Philippe Renaud, Alexandra Ros

    http://dx.doi.org/10.1002/elps.201200447 journal-article Martinez-Duarte, R. et al., 2013. Dielectrophoresis of lambda-DNA using 3D carbon electrodes. ELECTROPHORESIS, 34(7), pp.1113–1122. Available at: http://dx.doi.org/10.1002/elps.201200447. Rodrigo Martinez-Duarte and Fernanda …

  59. Dielectrophoresis: From molecular to micrometer scale analytes

    0.0 out of 5 stars 

    27 Nov 2018 | BioXFEL Publications | Contributor(s): Daihyun Kim, Mukul Sonker, Alexandra Ros

    http://dx.doi.org/10.1021/acs.analchem.8b05454 journal-article Kim, D., Sonker, M. & Ros, A., 2018. Dielectrophoresis: From molecular to micrometer scale analytes. Analytical Chemistry. Available at: http://dx.doi.org/10.1021/acs.analchem.8b05454. Daihyun Kim and Mukul Sonker and Alexandra Ros

  60. Dielectrophoretic Sorting of Membrane Protein Nanocrystals

    0.0 out of 5 stars 

    04 Sep 2013 | BioXFEL Publications | Contributor(s): Bahige G. Abdallah, Tzu-Chiao Chao, Christopher Kupitz, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1021/nn403760q Bahige G. Abdallah and Tzu-Chiao Chao and Christopher Kupitz and Petra Fromme and Alexandra Ros Abdallah, B.G. et al., 2013. Dielectrophoretic Sorting of Membrane Protein Nanocrystals. ACS Nano, 7(10), pp.9129–9137. Available at: …

  61. Difference structures from time-resolved small-angle and wide-angle x-ray scattering

    0.0 out of 5 stars 

    17 May 2018 | BioXFEL Publications | Contributor(s): Prakash Nepal, D. K. Saldin

    http://dx.doi.org/10.1103/physrevb.97.195426 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Nepal, P. & Saldin, D.K., 2018. Difference structures from time-resolved small-angle and wide-angle x-ray scattering. Physical Review B, 97(19). Available at: …

  62. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates

    0.0 out of 5 stars 

    12 Jan 2020 | BioXFEL Publications | Contributor(s): Benjamin A. Barad, Lin Liu, Roberto E. Diaz, Ralp Basilio, Steven J. Van Dyken, Richard M. Locksley, James Fraser

    http://dx.doi.org/10.1002/pro.3822 journal-article Barad, B.A. et al., 2020. Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein Science. Available at: http://dx.doi.org/10.1002/pro.3822. Benjamin A. Barad and Lin Liu and Roberto E. Diaz …

  63. Diffraction before destruction

    0.0 out of 5 stars 

    09 Jun 2014 | BioXFEL Publications | Contributor(s): H. N. Chapman, C. Caleman, N. Timneanu

    http://dx.doi.org/10.1098/rstb.2013.0313 H. N. Chapman and C. Caleman and N. Timneanu Chapman, H.N., Caleman, C. & Timneanu, N., 2014. Diffraction before destruction. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1647), pp.20130313–20130313. Available at: …

  64. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

    0.0 out of 5 stars 

    19 Nov 2020 | BioXFEL Publications | Contributor(s): Haoyuan Li, Reza Nazari, Brian Abbey, Roberto Alvarez, Andrew Aquila, Kartik Ayyer, Anton Barty, Peter Berntsen, Johan Bielecki, Alberto Pietrini, Maximilian Bucher, Gabriella Carini, Henry Chapman, Alice Contreras, Benedikt J. Daurer, Hasan Demirci, Leonie Flűckiger, Matthias Frank, Janos Hajdu, Max F. Hantke, Brenda Hogue, Ahmad Hosseinizadeh, Mark S. Hunter, H. Olof Jönsson, Richard Kirian, Ruslan P. Kurta, Duane Loh, Filipe R. N. C. Maia, Adrian P. Mancuso, Andrew J. Morgan, Matthew McFadden, Kerstin Muehlig, Anna Munke, Hemanth Kumar Narayana Reddy, Carl Nettelblad, Abbas Ourmazd, Max Rose, Peter Schwander, M. Marvin Seibert, Jonas A. Sellberg, Raymond G. Sierra, Zhibin Sun, Martin Svenda, Ivan A. Vartanyants, Peter Walter, Daniel Westphal, Garth Williams, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare

    http://dx.doi.org/10.1038/s41597-020-00745-2 AbstractSingle Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 …

  65. Diffraction data of core-shell nanoparticles from an X-ray free electron laser

    0.0 out of 5 stars 

    11 Apr 2017 | BioXFEL Publications | Contributor(s): Xuanxuan Li, Chun-Ya Chiu, Hsiang-Ju Wang, Stephan Kassemeyer, Sabine Botha, Robert L. Shoeman, Robert M Lawrence, Christopher Kupitz, Richard Kirian, Daniel James, Dingjie Wang, Garrett Charles Nelson, Marc Messerschmidt, Sébastien Boutet, Garth J. Williams, Elisabeth Hartmann, Aliakbar Jafarpour, Lutz M. Foucar, Anton Barty, Henry Chapman, Mengning Liang, Andreas Menzel, Fenglin Wang, Shibom Basu, Raimund Fromme, R. Bruce Doak, Petra Fromme, Uwe Weierstall, Michael H. Huang, John Spence, Ilme Schlichting, Brenda Hogue, Haiguang Liu

    http://dx.doi.org/10.1038/sdata.2017.48 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Li, X. et al., 2017. Diffraction data of core-shell nanoparticles from an X-ray free electron laser. Scientific Data, 4, p.170048. Available at: http://dx.doi.org/10.1038/sdata.2017.48. …

  66. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins

    0.0 out of 5 stars 

    18 Apr 2015 | BioXFEL Publications | Contributor(s): Michael E. Wall, Thomas C. Terwilliger, James Fraser, Paul D. Adams, Nicholas K. Sauter, Andrew VanBenschoten

    http://dx.doi.org/10.1016/j.bpj.2013.11.2171 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering for Ensemble Modeling of Crystalline Proteins. Biophysical Journal, 106(2), p.384a. Available at: http://dx.doi.org/10.1016/j.bpj.2013.11.2171. Michael E. Wall and Thomas C. Terwilliger …

  67. Diffuse X-Ray Scattering to Model Protein Motions

    0.0 out of 5 stars 

    04 Feb 2014 | BioXFEL Publications | Contributor(s): Michael E. Wall, Paul D. Adams, James S. Fraser, Nicholas K. Sauter

    http://dx.doi.org/10.1016/j.str.2014.01.002 journal-article Wall, M.E. et al., 2014. Diffuse X-Ray Scattering to Model Protein Motions. Structure, 22(2), pp.182–184. Available at: http://dx.doi.org/10.1016/j.str.2014.01.002. Michael E. Wall and Paul D. Adams and James S. Fraser and …

  68. Diffusion in multilayers, studied by quantitative chemical mapping at the atomic level

    0.0 out of 5 stars 

    18 Jun 2020 | BioXFEL Publications | Contributor(s): Y. Kim, A. Ourmazd

    http://dx.doi.org/10.1017/s0424820100174904 Using chemical lattice imaging in combination with vector pattern recognition, we study diffusion and interdiffusion at single interfaces in mulilayered semiconductors quantitatively with atomic plane resolution. 20 periods of 50Å C-doped GaAs/50Å …

  69. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology

    0.0 out of 5 stars 

    24 Feb 2023 | BioXFEL Publications | Contributor(s): Christian B. Macdonald, David Nedrud, Patrick Rockefeller Grimes, Donovan Trinidad, James Fraser, Willow Coyote-Maestas

    http://dx.doi.org/10.1186/s13059-023-02880-6 AbstractInsertions and deletions (indels) enable evolution and cause disease. Due to technical challenges, indels are left out of most mutational scans, limiting our understanding of them in disease, biology, and evolution. We develop a low cost and bias …

  70. Direct Observation of the Mechanism of Antibiotic Resistance by Mix-and-Inject at the European XFEL

    0.0 out of 5 stars 

    26 Nov 2020 | BioXFEL Publications | Contributor(s): Suraj Pandey, George Douglas Calvey, Andrea Katz, Tek Narsingh Malla, Faisal Hammad Mekky Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara Zielinski, Saša Bajt, Salah Awel, Katerina Dörner, Matthias Frank, Luca Gelisio, Rebecca Jeanne Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell Miller, Grant Mills, Garrett Charles Nelson, Jose L. Olmos, Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John Spence, Peter Schwander, Anton Barty, Henry Chapman, Petra Fromme, Adrian P. Mancuso, George Phillips, Richard Bean, Lois Pollack, Marius Schmidt

    http://dx.doi.org/10.1101/2020.11.24.396689 AbstractIn this study, we follow the diffusion and buildup of occupancy of the substrate ceftriaxone in M. tuberculosis β-lactamase BlaC microcrystals by structural analysis of the enzyme substrate complex at single millisecond time resolution. We also …

  71. Direct phasing in femtosecond nanocrystallography. I. Diffraction characteristics

    0.0 out of 5 stars 

    15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

    X-ray free-electron lasers solve a number of difficulties in protein crystallography by providing intense but ultra-short pulses of X-rays, allowing collection of useful diffraction data from nanocrystals. Whereas the diffraction from large crystals corresponds only to samples of the Fourier …

  72. Direct phasing in femtosecond nanocrystallography. II. Phase retrieval

    0.0 out of 5 stars 

    15 Jan 2014 | BioXFEL Publications | Contributor(s): Joe Chen, John Spence, Rick P. Millane

    X-ray free-electron laser diffraction patterns from protein nanocrystals provide information on the diffracted amplitudes between the Bragg reflections, offering the possibility of direct phase retrieval without the use of ancillary experimental diffraction data [Spenceet al.(2011).Opt. Express,19, …

  73. Direct Phasing of Finite Crystals Illuminated with a Free-Electron Laser

    0.0 out of 5 stars 

    12 Feb 2015 | BioXFEL Publications | Contributor(s): Richard Kirian, Richard J. Bean, Kenneth R. Beyerlein, Miriam Barthelmess, Chun Hong Yoon, Fenglin Wang, Flavio Capotondi, Emanuele Pedersoli, Anton Barty, Henry Chapman

    http://dx.doi.org/10.1103/physrevx.5.011015 Richard A. Kirian and Richard J. Bean and Kenneth R. Beyerlein and Miriam Barthelmess and Chun Hong Yoon and Fenglin Wang and Flavio Capotondi and Emanuele Pedersoli and Anton Barty and Henry N. Chapman Kirian, R.A. et al., 2015. Direct Phasing of …

  74. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy

    0.0 out of 5 stars 

    06 Mar 2018 | BioXFEL Publications | Contributor(s): GANESH SUBRAMANIAN, Xiaoyi Zhang, Gerdenis Kodis, Qingyu Kong, Cunming Liu, Andrew Chizmeshya, Uwe Weierstall, John Spence

    http://dx.doi.org/10.1021/acs.jpclett.8b00083 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Subramanian, G. et al., 2018. Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy. The …

  75. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

    0.0 out of 5 stars 

    11 Jan 2022 | BioXFEL Publications | Contributor(s): Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris Diane Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James Fraser, Dan S Tawfik, Danica Galonić Fujimori

    http://dx.doi.org/10.7554/elife.70017 Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, …

  76. Discovering Design Principles to Re-Engineer Functional RNA Elements

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Alex Plumridge, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.556 poster Plumridge, A. & Pollack, L., 2020. Discovering Design Principles to Re-Engineer Functional RNA Elements. Biophysical Journal, 118(3), p.70a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.556. Alex Plumridge and Lois Pollack

  77. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine

    0.0 out of 5 stars 

    25 Sep 2014 | BioXFEL Publications | Contributor(s): Brianna B. Williams, Andrew H. Van Benschoten, Peter Cimermancic, Mohamed S. Donia, Michael Zimmermann, Mao Taketani, Atsushi Ishihara, Purna C. Kashyap, James S. Fraser, Michael A. Fischbach

    http://dx.doi.org/10.1016/j.chom.2014.09.001 journal-article Williams, B.B. et al., 2014. Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine. Cell Host & Microbe, 16(4), pp.495–503. Available at: …

  78. Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia

    0.0 out of 5 stars 

    02 Nov 2023 | BioXFEL Publications | Contributor(s): Andreas Varkaris, Ermira Pazolli, Hakan Gunaydin, Qi Wang, Levi Pierce, Alessandro A. Boezio, Artemisa Bulku, Lucian DiPietro, Cary Fridrich, Adam Frost, Fabrizio Giordanetto, Erika P. Hamilton, Katherine Harris, Michael Holliday, Tamieka L. Hunter, Amanda Iskandar, Yongli Ji, Alexandre Larivée, Jonathan R. LaRochelle, André Lescarbeau, Fabien Llambi, Brenda Lormil, Mary M. Mader, Brenton G. Mar, Iain Martin, Thomas H. McLean, Klaus Michelsen, Yakov Pechersky, Erika Puente-Poushnejad, Kevin Raynor, Dipali Rogala, Ramin Samadani, Alison M. Schram, Kelley Shortsleeves, Sweta Swaminathan, Shahein Tajmir, Gege Tan, Yong Tang, Roberto Valverde, Bryan Wehrenberg, Jeremy Wilbur, Bret R. Williams, Hongtao Zeng, Hanmo Zhang, W. Patrick Walters, Beni B. Wolf, David E. Shaw, Donald A. Bergstrom, James Watters, James Fraser, Pascal D. Fortin, D. Randal Kipp

    http://dx.doi.org/10.1158/2159-8290.cd-23-0944 Abstract PIK3CA (PI3Kα) is a lipid kinase commonly mutated in cancer, including ∼40% of hormone receptor–positive breast cancer. The most frequently observed mutants occur in the kinase and …

  79. Discovery of allosteric binding sites by crystallographic fragment screening

    0.0 out of 5 stars 

    07 Nov 2020 | BioXFEL Publications | Contributor(s): Tobias Krojer, James Fraser, Frank Von Delft

    http://dx.doi.org/10.1016/j.sbi.2020.08.004 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Krojer, T., Fraser, J.S. & von Delft, F., 2020. Discovery of allosteric binding sites by crystallographic fragment screening. Current Opinion in Structural Biology, 65, pp.209–216. …

  80. Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD

    0.0 out of 5 stars 

    11 Feb 2022 | BioXFEL Publications | Contributor(s): Alexis M. Kelley, Christian B. Macdonald, James Fraser

    http://dx.doi.org/10.1016/j.bpj.2021.11.2487 journal-article Kelley, A. M., Macdonald, C. B., & Fraser, J. (2022). Dismantling antibiotic resistance one variant at a time: in vitro and computational analysis of VatD. Biophysical Journal, 121(3), 48a. https://doi.org/10.1016/j.bpj.2021.11.2487 …

  81. Distinct conformational states enable transglutaminase 2 to promote cancer cell survival versus cell death

    0.0 out of 5 stars 

    12 Aug 2024 | BioXFEL Publications | Contributor(s): Cody Aplin, Kara Zielinski, Suzette Pabit, Deborah Ogunribido, William P. Katt, Lois Pollack, Richard A. Cerione, Shawn K. Milano

    https://doi.org/10.1038/s42003-024-06672-x AbstractTransglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states …

  82. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure

    0.0 out of 5 stars 

    25 Sep 2018 | BioXFEL Publications | Contributor(s): Robb Welty, Suzette A. Pabit, Andrea Katz, George Douglas Calvey, Lois Pollack, Kathleen B. Hall

    http://dx.doi.org/10.1261/rna.068361.118 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Welty, R. et al., 2018. Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure. RNA, 24(12), pp.1828–1838. Available at: …

  83. DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles

    0.0 out of 5 stars 

    15 Feb 2019 | BioXFEL Publications | Contributor(s): Alex Mauney, Joshua Tokuda, Yujie Chen, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2018.11.1179 poster Mauney, A. et al., 2019. DNA Sequence and Histone Core Composition Control the Unwrapping of DNA from Nucleosome Core Particles. Biophysical Journal, 116(3), p.214a. Available at: http://dx.doi.org/10.1016/j.bpj.2018.11.1179. Alex Mauney and …

  84. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes

    0.0 out of 5 stars 

    07 Feb 2020 | BioXFEL Publications | Contributor(s): Alex Mauney, Lois Pollack

    http://dx.doi.org/10.1016/j.bpj.2019.11.2706 poster Mauney, A. & Pollack, L., 2020. DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes. Biophysical Journal, 118(3), p.489a. Available at: http://dx.doi.org/10.1016/j.bpj.2019.11.2706. Alex Mauney and Lois …

  85. Dose efficient Compton X-ray microscopy

    0.0 out of 5 stars 

    10 Apr 2018 | BioXFEL Publications | Contributor(s): P. Villanueva-Perez, S. Bajt, H. N. Chapman

    http://dx.doi.org/10.1364/optica.5.000450 journal-article Villanueva-Perez, P., Bajt, S. & Chapman, H.N., 2018. Dose efficient Compton X-ray microscopy. Optica, 5(4), p.450. Available at: http://dx.doi.org/10.1364/optica.5.000450. P. Villanueva-Perez and S. Bajt and H. N. Chapman

  86. Double-flow focused liquid injector for efficient serial femtosecond crystallography

    0.0 out of 5 stars 

    16 Mar 2017 | BioXFEL Publications | Contributor(s): Dominik Oberthuer, Juraj Knoška, Max Oliver Wiedorn, Kenneth R. Beyerlein, David Bushnell, Elena G. Kovaleva, Michael Heymann, Lars Gumprecht, Richard Kirian, Anton Barty, Valerio Mariani, Aleksandra Tolstikova, Luigi Adriano, Salah Awel, Miriam Barthelmess, Katerina Dörner, P. Lourdu Xavier, Oleksandr Yefanov, Daniel R. James, Garrett Charles Nelson, Dingjie Wang, George Douglas Calvey, Yujie Chen, Andrea Schmidt, Michael Szczepek, Stefan Frielingsdorf, Oliver Lenz, Edward Snell, Philip J. Robinson, Božidar Šarler, Grega Belšak, Marjan Maček, Fabian Wilde, Andrew Aquila, Sébastien Boutet, Mengning Liang, Mark S. Hunter, Patrick Scheerer, John D. Lipscomb, Uwe Weierstall, Roger Kornberg, John Spence, Lois Pollack, Henry Chapman, Saša Bajt

    http://dx.doi.org/10.1038/srep44628 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Oberthuer, D. et al., 2017. Double-flow focused liquid injector for efficient serial femtosecond crystallography. Scientific Reports, 7, p.44628. Available at: http://dx.doi.org/10.1038/srep44628. …

  87. Double-focusing mixing jet for XFEL study of chemical kinetics

    0.0 out of 5 stars 

    06 Oct 2014 | BioXFEL Publications | Contributor(s): Dingjie Wang, Uwe Weierstall, Lois Pollack, John Spence

    Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

  88. Double-focusing mixing jet for XFEL study of chemical kinetics

    0.0 out of 5 stars 

    13 Oct 2015 | Teaching Materials

    Several liquid sample injection methods have been developed to satisfy the requirements for serial femtosecond X-ray nanocrystallography, which enables radiation-damage-free determination of molecular structure at room temperature. Time-resolved nanocrystallography would combine structure analysis …

  89. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation

    0.0 out of 5 stars 

    07 Feb 2014 | BioXFEL Publications | Contributor(s): R. Paul, R. E. Jinkerson, K. Buss, J. Steel, R. Mohr, W. R. Hess, M. Chen, P. Fromme

    journal-article http://dx.doi.org/10.1128/genomea.01166-13 Paul, R. et al., 2014. Draft Genome Sequence of the Filamentous Cyanobacterium Leptolyngbya sp. Strain Heron Island J, Exhibiting Chromatic Acclimation. Genome Announcements, 2(1), pp.e01166–13–e01166–13. Available at: …

  90. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers

    0.0 out of 5 stars 

    02 Mar 2017 | BioXFEL Publications | Contributor(s): Franklin D Fuller, Sheraz Gul, Ruchira Chatterjee, E Sethe Burgie, Iris Diane Young, Hugo Lebrette, Vivek Srinivas, Aaron S Brewster, Tara Michels-Clark, Jonathan Clinger, Babak Andi, Mohamed Ibrahim, Ernest Pastor, Casper De Lichtenberg, Rana Hussein, Christopher J Pollock, Miao Zhang, Claudiu A Stan, Thomas Kroll, Thomas Fransson, Clemens Weninger, Markus Kubin, Pierre Aller, Louise Lassalle, Philipp Bräuer, Mitchell Miller, Muhamed Amin, Sergey Koroidov, Christian G Roessler, Marc Allaire, Raymond G Sierra, Peter T Docker, James M Glownia, Silke Nelson, Jason E Koglin, Diling Zhu, Matthieu Chollet, Sanghoon Song, Henrik Lemke, Mengning Liang, Dimosthenis Sokaras, Roberto Alonso-Mori, Athina Zouni, Johannes Messinger, Uwe Bergmann, Amie K Boal, J Martin Bollinger, Carsten Krebs, Martin Högbom, George Phillips, Richard D Vierstra, Nicholas K Sauter, Allen M Orville, Jan Kern, Vittal K Yachandra, Junko Yano

    journal-article http://dx.doi.org/10.1038/nmeth.4195 NSF-STC Biology with X-ray Lasers (NSF-1231306) Fuller, F.D. et al., 2017. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nature Methods, 14(4), pp.443–449. Available at: …

  91. Dynamics from noisy data with extreme timing uncertainty

    0.0 out of 5 stars 

    26 Apr 2016 | BioXFEL Publications | Contributor(s): R. Fung, A. Ourmazd, A. M. Hanna, O. Vendrell, S. Ramakrishna, T. Seideman, R. Santra

    http://dx.doi.org/10.1038/nature17627 R. Fung and A. Ourmazd and A. M. Hanna and O. Vendrell and S. Ramakrishna and T. Seideman and R. Santra and A. Ourmazd Fung, R. et al., 2016. Dynamics from noisy data with extreme timing uncertainty. Nature, 532(7600), pp.471–475. Available at: …

  92. Dynamics of rare gas solids irradiated by electron beams

    0.0 out of 5 stars 

    10 Apr 2020 | BioXFEL Publications | Contributor(s): J. Candanedo, C. Caleman, N. Tîmneanu, O. Beckstein, J. C. H. Spence

    http://dx.doi.org/10.1063/1.5134801 journal-article Candanedo, J. et al., 2020. Dynamics of rare gas solids irradiated by electron beams. The Journal of Chemical Physics, 152(14), p.144303. Available at: http://dx.doi.org/10.1063/1.5134801. J. Candanedo and C. Caleman and N. Tîmneanu and O. …

  93. Dynamics retrieval from stochastically weighted incomplete data by low-pass spectral analysis

    0.0 out of 5 stars 

    16 Aug 2022 | BioXFEL Publications | Contributor(s): Cecilia M. Casadei, Ahmad Hosseinizadeh, Gebhard F.X. Schertler, Abbas Ourmazd, Robin Santra

    http://dx.doi.org/10.1063/4.0000156 Time-resolved serial femtosecond crystallography (TR-SFX) provides access to protein dynamics on sub-picosecond timescales, and with atomic resolution. Due to the nature of the experiment, these datasets are often highly incomplete and the measured diffracted …

  94. E pluribus unum, no more: from one crystal, many conformations

    0.0 out of 5 stars 

    09 Aug 2014 | BioXFEL Publications | Contributor(s): Rahel Woldeyes, David A Sivak, James Fraser

    http://dx.doi.org/10.1016/j.sbi.2014.07.005 Rahel A Woldeyes and David A Sivak and James S Fraser Woldeyes, R.A., Sivak, D.A. & Fraser, J.S., 2014. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology, 28, pp.56–62. Available at: …

  95. Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

    0.0 out of 5 stars 

    22 Mar 2021 | BioXFEL Publications | Contributor(s): Ji-Hye Yun, Xuanxuan Li, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia Zatsepin, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park, John Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu

    http://dx.doi.org/10.1073/pnas.2020486118 Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial …

  96. Editorial overview: Biophysical and molecular biological methods

    0.0 out of 5 stars 

    28 Nov 2016 | BioXFEL Publications | Contributor(s): Petra Fromme, Andrej Sali

    http://dx.doi.org/10.1016/j.sbi.2016.11.015 journal-article Fromme, P. & Sali, A., 2016. Editorial overview: Biophysical and molecular biological methods. Current Opinion in Structural Biology, 40, pp.ix–xi. Available at: http://dx.doi.org/10.1016/j.sbi.2016.11.015. Petra Fromme and Andrej Sali

  97. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases

    0.0 out of 5 stars 

    13 Jun 2014 | BioXFEL Publications | Contributor(s): Sojin Moon, Ryan M. Bannen, Thomas J. Rutkoski, George Phillips, Euiyoung Bae

    http://dx.doi.org/10.1002/prot.24627 journal-article Moon, S. et al., 2014. Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins: Structure, Function, and Bioinformatics, 82(10), …

  98. Effectiveness of different types of Masks in Aerosol Dispersion in SARS–CoV-2 Infection

    0.0 out of 5 stars 

    17 Jun 2021 | BioXFEL Publications | Contributor(s): Gokhan Tanisali, Ahmet Sozak, Abdul Samet Bulut, Tolga Ziya Sander, Ozlem Dogan, Çağdaş Dağ, Mehmet Gönen, Fusun Can, Hasan Demirci, Onder Ergonul

    http://dx.doi.org/10.1016/j.ijid.2021.06.029 journal-article Tanisali, G. et al., 2021. Effectiveness of different types of Masks in Aerosol Dispersion in SARS–CoV-2 Infection. International Journal of Infectious Diseases. Available at: http://dx.doi.org/10.1016/j.ijid.2021.06.029. Gokhan …

  99. Effects of self-seeding and crystal post-selection on the quality of Monte Carlo-integrated SFX data

    0.0 out of 5 stars 

    21 Apr 2015 | BioXFEL Publications | Contributor(s): Thomas Barends, Thomas A. White, Anton Barty, Lutz Foucar, Marc Messerschmidt, Roberto Alonso-Mori, Sabine Botha, Henry Chapman, R. Bruce Doak, Lorenzo Galli, Cornelius Gati, Matthias Gutmann, Jason Koglin, Anders Markvardsen, Karol Nass, Dominik Oberthur, Robert L. Shoeman, Ilme Schlichting, Sébastien Boutet

    Serial femtosecond crystallography (SFX) is an emerging method for data collection at free-electron lasers (FELs) in which single diffraction snapshots are taken from a large number of crystals. The partial intensities collected in this way are then combined in a scheme called Monte Carlo …

  100. Efficient Computation of k-Nearest Neighbour Graphs for Large High-Dimensional Data Sets on GPU Clusters

    0.0 out of 5 stars 

    23 Sep 2013 | BioXFEL Publications | Contributor(s): Ali Dashti, Ivan Komarov, Roshan M. D’Souza

    http://dx.doi.org/10.1371/journal.pone.0074113 journal-article Dashti, A., Komarov, I. & D’Souza, R.M., 2013. Efficient Computation of k-Nearest Neighbour Graphs for Large High-Dimensional Data Sets on GPU Clusters A. Gursoy, ed. PLoS ONE, 8(9), p.e74113. Available at: …