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  1. 'Hit and run' serial femtosecond crystallography of a membrane kinase in the lipid cubic phase

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): M. Caffrey, D. Li, N. Howe, S. T. A. Shah

    journal-article http://dx.doi.org/10.1098/rstb.2013.0621 NSF-STC Biology with X-ray Lasers (NSF-1231306) Caffrey, M. et al., 2014. “Hit and run” serial femtosecond crystallography of a membrane kinase in the lipid cubic phase. Philosophical Transactions of the Royal Society B: Biological …

  2. 1. Before your beamtime

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Advice for preparing for an LCLS beamtime, especially for data analysts.

  3. 2. During your beamtime

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Important tasks for data analysts during the LCLS beamtime.  Explanation of LCLS eLog.

  4. 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening

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    27 Feb 2023 | BioXFEL Publications | Contributor(s): Miranda Lynch, M. Elizabeth Snell, Stephen A. Potter, Edward Snell, Sarah EJ Bowman

    http://dx.doi.org/10.1107/s2059798323001274 Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which …

  5. 2014 Data Analysis Workshop

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    26 Aug 2014 | Workshops | Contributor(s): Tom Grant, Nadia Zatsepin

    Video and interactive web presentations with PDF slides available for download. Description Serial crystallography is a rapidly growing field with a correspondingly rapidly growing user base. One of the main bottlenecks in serial crystallography is the ability to efficiently filter and analyze …

  6. 2015 BioXFEL International Conference Invited Speakers Abstracts

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    17 Dec 2014 | Downloads

    This is a compilation of the abstracts of the Invited Speakers of the 2015 BioXFEL Conference in Ponce, Puerto Rico.  For more information please visit the event page www.bioxfel.org/events/details/6  

  7. 2015 HWI Crystallization Workshop

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    13 Oct 2015 | Workshops | Contributor(s): Tom Grant, Bill Bauer, Edward Snell

    Crystallization is the major bottleneck to 3D structure determination using X-ray crystallography. In this workshop we will discuss many tenets of successful crystallization for both conventional and serial crystallography. Many topics will be covered including fundamentals of crystal growth, …

  8. 2015 Phenix Workshop at Rice University

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    03 Apr 2015 | Workshops | Contributor(s): Tom Grant, George Phillips

    The Gulf Coast Consortia, BioXFEL, and Rice University present an instructional workshop on Phenix, the Python-based Hierarchical Environment for Intergrated Xtallography. Topics include experimental phasing, molecular replacement, model refinement and structure validation.

  9. 2015 Serial Crystallography Data Analysis Workshop at ACA Annual Meeting.

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    23 Apr 2015 | Workshops | Contributor(s): Nadia Zatsepin, Tom Grant

    We are running a serial femtosecond crystallography data analysis workshop at ACA 2015 in Philadelphia, PA, focused on "Serial Crystallography Data Analysis with Cheetah and CrystFEL: Concepts and Tutorials".  www.amercrystalassn.org/2015-wk.02   Workshop format: The workshop will start with an …

  10. 2015 Single Particle Imaging Workshop

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    17 Aug 2015 | Workshops | Contributor(s): Russell Fung

    How do you make a movie of a single particle jiggling and wiggling with atomic resolution and ultra-fast temporal resolution? How do you calculate the energy landscape or the kinetics/dynamics of a sequence of conformational changes? What do you do with millions and millions of snapshots, each for …

  11. 2016 Serial Crystallography Data Analysis Workshop at ACA Annual Meeting.

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    31 Mar 2016 | Workshops

    We are running a serial femtosecond crystallography data analysis workshop at ACA 2016 in Denver, CO, focused on "Serial Crystallography Data Analysis with Cheetah and CrystFEL: Concepts and Tutorials".  ACA 2016 Workshop Site   Workshop format: The workshop will start with an introductory …

  12. 2022 Conference

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    07 Dec 2021 | Downloads

    …

  13. 2D Crystallography

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    06 May 2015 | Teaching Materials

    Dr. Mattias Frank discusses new possibilities in the field of 2D crystallography made possible by XFEL sources.

  14. 2nd International BioXFEL Conference Detailed Agenda

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    05 Dec 2014 | Downloads | Contributor(s): Tom Grant

    This is a detailed agenda for the 2nd International BioXFEL Conference to be held in Ponce, Puerto Rico in January 2015. For more details about the event and to register, visit https://www.bioxfel.org/events/details/6

  15. 2nd International BioXFEL Conference Logo

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    11 Jul 2014 | Downloads | Contributor(s): Tom Grant

    Transparent background logo for 2nd BioXFEL Conference

  16. 3. Accessing your data

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Where is your LCLS data? How long will it be there? 

  17. 3D diffractive imaging of nanoparticle ensembles using an x-ray laser

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    20 Nov 2020 | BioXFEL Publications | Contributor(s): Kartik Ayyer, P. Lourdu Xavier, Johan Bielecki, Zhou Shen, Benedikt J. Daurer, Amit K. Samanta, Salah Awel, Richard Bean, Anton Barty, Martin Bergemann, Tomas Ekeberg, Armando D. Estillore, Hans Fangohr, Klaus Giewekemeyer, Mark S. Hunter, Mikhail Karnevskiy, Richard Kirian, Henry Kirkwood, Yoonhee Kim, Jayanath Koliyadu, Holger Lange, Romain Letrun, Jannik Lübke, Thomas Michelat, Andrew J. Morgan, Nils Roth, Tokushi Sato, Marcin Sikorski, Florian Schulz, John Spence, Patrik Vagovic, Tamme Wollweber, Lena Worbs, Oleksandr Yefanov, Yulong Zhuang, Filipe R. N. C. Maia, Daniel A. Horke, Jochen Küpper, N. Duane Loh, Adrian P. Mancuso, Henry Chapman

    http://dx.doi.org/10.1364/optica.410851 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Ayyer, K. et al., 2020. 3D diffractive imaging of nanoparticle ensembles using an x-ray laser. Optica, 8(1), p.15. Available at: http://dx.doi.org/10.1364/optica.410851. Kartik Ayyer and P. …

  18. 3D printed droplet generation devices for serial femtosecond crystallography enabled by surface coating

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    29 Aug 2019 | BioXFEL Publications | Contributor(s): Austin Echelmeier, Daihyun Kim, Jorvani Cruz Villarreal, Jesse David Coe, Sebastian E Quintana, Gerrit Brehm, Ana Egatz-Gomez, Reza Nazari, Raymond G. Sierra, Jason E. Koglin, Alexander Batyuk, Mark S. Hunter, Sébastien Boutet, Nadia Zatsepin, Richard Kirian, Thomas D. Grant, Petra Fromme, Alexandra Ros

    http://dx.doi.org/10.1107/s1600576719010343 The role of surface wetting properties and their impact on the performance of 3D printed microfluidic droplet generation devices for serial femtosecond crystallography (SFX) are reported. SFX is a novel crystallography method enabling structure …

  19. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets

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    26 Jun 2020 | BioXFEL Publications | Contributor(s): Reza Nazari, Sahba Zaare, Roberto C. Alvarez, Konstantinos Karpos, Trent Engelman, Caleb Alexander Madsen, Garrett Charles Nelson, John Spence, Uwe Weierstall, Ronald J. Adrian, Richard Kirian

    http://dx.doi.org/10.1364/oe.390131 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Nazari, R. et al., 2020. 3D printing of gas-dynamic virtual nozzles and optical characterization of high-speed microjets. Optics Express, 28(15), p.21749. Available at: …

  20. 3D Single Particle Structure Recovery

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    07 Oct 2015 | Teaching Materials | Contributor(s): Ahmad Hosseinizadeh

    Dr. Ahmad Hosseinizadeh discuss different pathways to recovering the structure of single particles from XFEL snapshots.

  21. 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow

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    16 Jan 2020 | BioXFEL Publications | Contributor(s): Diana Monteiro, David Von Stetten, Claudia Stohrer, Marta Sans, Arwen R. Pearson, Gianluca Santoni, Peter Van Der Linden, Martin Trebbin

    http://dx.doi.org/10.1107/s2052252519016865 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of …

  22. 3rd BioXFEL International Conference

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    08 Sep 2015 | Downloads

    …

  23. 4. Detectors and geometry

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    CXI detectors and geometry

  24. 4th BioXFEL Conference

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    04 Nov 2016 | Downloads

    …

  25. 5. Data reduction and hit finding

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin, Richard A Kirian

    LCLS data reduction and hit finding. Running Cheetah at LCLS. Tuning hit finding parameters and understanding Cheetah's output.

  26. 5th BioXFEL International Conference

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    04 Dec 2017 | Downloads

    …

  27. 6. Live data monitoring and interactive hit finding refinement: OnDA

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    OnDA - live data monitoring and interactive hit finding refinement

  28. 7 A resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

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    09 Jun 2014 | BioXFEL Publications | Contributor(s): B. Pedrini, C.-J. Tsai, G. Capitani, C. Padeste, M. S. Hunter, N. A. Zatsepin, A. Barty, W. H. Benner, S. Boutet, G. K. Feld, S. P. Hau-Riege, R. A. Kirian, C. Kupitz, M. Messerschmitt, J. I. Ogren, T. Pardini, B. Segelke, G. J. Williams, J. C. H. Spence, R. Abela, M. Coleman, J. E. Evans, G. F. X. Schertler, M. Frank, X.-D. Li

    http://dx.doi.org/10.1098/rstb.2013.0500 B. Pedrini and C.-J. Tsai and G. Capitani and C. Padeste and M. S. Hunter and N. A. Zatsepin and A. Barty and W. H. Benner and S. Boutet and G. K. Feld and S. P. Hau-Riege and R. A. Kirian and C. Kupitz and M. Messerschmitt and J. I. Ogren and T. Pardini and …

  29. 7. Working with LCLS data remotely

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Working with LCLS data remotely

  30. 7th Annual BioXFEL International Conference

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    23 May 2019 | Downloads

    …

  31. 7th Annual BioXFEL International Conference

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    23 Dec 2019 | Downloads

    …

  32. 8. Managing and copying LCLS data

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    LCLS data management and transfer.

  33. 8th BioXFEL International Conference

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    09 Dec 2020 | Downloads

    …

  34. 9. Indexing, merging, evaluation crystal diffraction data: CrystFEL

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    21 Jul 2015 | Series | Contributor(s): Nadia Zatsepin

    Indexing, merging, evaluation serial crystallography data

  35. In situ counter-diffusion crystallization and long-term crystal preservation in microfluidic fixed targets for serial crystallography

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    25 Sep 2024 | BioXFEL Publications | Contributor(s): Zhongrui Liu, Kevin Gu, Megan Shelby, Debdyuti Roy, SRINIVASAN MUNIYAPPAN, Marius Schmidt, Sankar Raju Narayanasamy, Matthew Coleman, Matthias Frank, Tonya L. Kuhl

    https://doi.org/10.1107/s1600576724007544 Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in …

  36. CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention

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    14 Aug 2024 | BioXFEL Publications | Contributor(s): Tom Pan, Chen Dun, Shikai Jin, Mitchell Miller, Anastasios Kyrillidis, George Phillips

    https://doi.org/10.1063/4.0000252 Determining the atomic-level structure of a protein has been a decades-long challenge. However, recent advances in transformers and related neural network architectures have enabled researchers to significantly improve solutions to this problem. These methods use …

  37. A Brief Atlas of Insulin

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    13 Jun 2022 | BioXFEL Publications | Contributor(s): Hasan Demirci, Esra Ayan

    http://dx.doi.org/10.2174/1573399819666220610150342 Abstract: Insulin is an essential factor for mammalian organisms: a regulator of glucose metabolism and other key signaling pathways. Insulin is also a multifunctional hormone whose absence can cause many diseases. Recombinant insulin is widely …

  38. A Brief History of Electron Microdiffraction

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    09 Jun 2013 | BioXFEL Publications | Contributor(s): J. C. H. Spence, J. M. Zuo

    http://dx.doi.org/10.1007/978-1-4899-2353-0_1 book-chapter Spence, J.C.H. & Zuo, J.M., 1992. A Brief History of Electron Microdiffraction. Electron Microdiffraction, pp.1–5. Available at: http://dx.doi.org/10.1007/978-1-4899-2353-0_1. J. C. H. Spence and J. M. Zuo

  39. A Bright Future for Serial Femtosecond Crystallography with XFELs

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    18 Jul 2017 | BioXFEL Publications | Contributor(s): Linda C. Johansson, Benjamin Stauch, Andrii Ishchenko, Vadim Cherezov

    http://dx.doi.org/10.1016/j.tibs.2017.06.007 journal-article Johansson, L.C. et al., 2017. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends in Biochemical Sciences. Available at: http://dx.doi.org/10.1016/j.tibs.2017.06.007. Linda C. Johansson and Benjamin Stauch and …

  40. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening

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    14 Jun 2021 | BioXFEL Publications | Contributor(s): Shuo Sui, Anne Mulichak, Raviraj Kulathila, Joshua McGee, Danny Filiatreault, Sarthak Saha, Aina Cohen, Jinhu Song, Holly Hung, Jonathan Selway, Christina Kirby, Om K. Shrestha, Wilhelm Weihofen, Michelle Fodor, Mei Xu, Rajiv Chopra, Sarah Perry

    http://dx.doi.org/10.1107/s1600576721004155 A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable …

  41. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis

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    20 Dec 2021 | BioXFEL Publications | Contributor(s): Vijay Jayaraman, D. John Lee, Nadav Elad, Shay Vimer, Michal Sharon, James Fraser, Dan S. Tawfik

    http://dx.doi.org/10.1038/s41589-021-00919-y journal-article Jayaraman, V., Lee, D. J., Elad, N., Vimer, S., Sharon, M., Fraser, J. S., & Tawfik, D. S. (2021). A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nature Chemical Biology, 18(2), 161–170. …

  42. A data set from flash X-ray imaging of carboxysomes

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    29 Jul 2016 | BioXFEL Publications | Contributor(s): Max F. Hantke, Dirk Hasse, Tomas Ekeberg, Katja John, Martin Svenda, Duane Loh, Andrew V. Martin, Nicusor Timneanu, Daniel S.D. Larsson, Gijs Van Der Schot, Gunilla H. Carlsson, Margareta Ingelman, Jakob Andreasson, Daniel Westphal, Bianca Iwan, Charlotte Uetrecht, Johan Bielecki, Mengning Liang, Francesco Stellato, Daniel P. DePonte, Sadia Bari, Robert Hartmann, Nils Kimmel, Richard Kirian, M. Marvin Seibert, Kerstin Mühlig, Sebastian Schorb, Ken Ferguson, Christoph Bostedt, Sebastian Carron, John D. Bozek, Daniel Rolles, Artem Rudenko, Lutz Foucar, Sascha W. Epp, Henry Chapman, Anton Barty, Inger Andersson, Janos Hajdu, Filipe R.N.C. Maia

    http://dx.doi.org/10.1038/sdata.2016.61 Max F. Hantke and Dirk Hasse and Tomas Ekeberg and Katja John and Martin Svenda and Duane Loh and Andrew V. Martin and Nicusor Timneanu and Daniel S.D. Larsson and Gijs van der Schot and Gunilla H. Carlsson and Margareta Ingelman and Jakob Andreasson and …

  43. A deep learning solution for crystallographic structure determination

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    25 May 2023 | BioXFEL Publications | Contributor(s): Tom Pan, Shikai Jin, Mitchell Miller, Anastasios Kyrillidis, George Phillips

    http://dx.doi.org/10.1107/s2052252523004293 The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallography, …

  44. A fixed-target platform for serial femtosecond crystallography in a hydrated environment

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    21 Nov 2019 | BioXFEL Publications | Contributor(s): M. L. Shelby, D. Gilbile, T. D. Grant, C. Seuring, B. W. Segelke, W. He, A. C. Evans, T. Pakendorf, P. Fischer, M. S. Hunter, A. Batyuk, M. Barthelmess, A. Meents, M. A. Coleman, T. L. Kuhl, M. Frank

    http://dx.doi.org/10.1107/s2052252519014003 For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while …

  45. A generalized parametric divisor method for political apportionment

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    14 Dec 2018 | BioXFEL Publications | Contributor(s): Tatsuo Oyama, Nicholas G. Hall, Kazuhiro Kobayashi

    http://dx.doi.org/10.1111/itor.12622 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Oyama, T., Hall, N.G. & Kobayashi, K., 2018. A generalized parametric divisor method for political apportionment. International Transactions in Operational Research, 28(1), pp.327–355. Available …

  46. A glycan gate controls opening of the SARS-CoV-2 spike protein

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    19 Aug 2021 | BioXFEL Publications | Contributor(s): Terra Sztain, Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, Evan Seitz, Ryan S. McCool, Fiona L. Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, J. Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S. McLellan, Lillian T. Chong, Rommie E. Amaro

    http://dx.doi.org/10.1038/s41557-021-00758-3 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sztain, T. et al., 2021. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nature Chemistry. Available at: http://dx.doi.org/10.1038/s41557-021-00758-3. Terra Sztain and …

  47. A Graphene-Based Microfluidic Platform for Electrocrystallization and In Situ X-ray Diffraction

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    02 Feb 2018 | BioXFEL Publications | Contributor(s): Shuo Sui, Yuxi Wang, Christos Dimitrakopoulos, Sarah Perry

    http://dx.doi.org/10.3390/cryst8020076 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Sui, S. et al., 2018. A Graphene-Based Microfluidic Platform for Electrocrystallization and In Situ X-ray Diffraction. Crystals, 8(2), p.76. Available at: http://dx.doi.org/10.3390/cryst8020076. …

  48. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta

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    12 Nov 2014 | BioXFEL Publications | Contributor(s): Paolo Rossi, Lei Shi, Gaohua Liu, Christopher M. Barbieri, Hsiau-Wei Lee, Thomas D. Grant, Joseph Luft, Rong Xiao, Thomas B. Acton, Edward Snell, Gaetano T. Montelione, David Baker, Oliver F. Lange, Nikolaos G. Sgourakis

    http://dx.doi.org/10.1002/prot.24719 journal-article Rossi, P. et al., 2014. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins: Structure, Function, and Bioinformatics, 83(2), pp.309–317. Available at: …

  49. A language model beats alphafold2 on orphans

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    03 Oct 2022 | BioXFEL Publications | Contributor(s): Jennifer M. Michaud, Ali Madani, James Fraser

    http://dx.doi.org/10.1038/s41587-022-01466-0 journal-article Michaud, J. M., Madani, A., & Fraser, J. S. (2022). A language model beats alphafold2 on orphans. Nature Biotechnology, 40(11), 1576–1577. https://doi.org/10.1038/s41587-022-01466-0 Jennifer M. Michaud and Ali Madani and James S. …

  50. A Metropolis Monte Carlo algorithm for merging single-particle diffraction intensities

    0.0 out of 5 stars 

    04 Apr 2022 | BioXFEL Publications | Contributor(s): B. R. Mobley, K. E. Schmidt, J. P. J. Chen, R. A. Kirian

    http://dx.doi.org/10.1107/s2053273322001395 Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The expand–maximize–compress (EMC) …

  51. A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS

    0.0 out of 5 stars 

    29 Jan 2015 | BioXFEL Publications | Contributor(s): Jesse B. Hopkins, Andrea Katz, Steve P. Meisburger, Matthew A. Warkentin, Robert E. Thorne, Lois Pollack

    http://dx.doi.org/10.1107/s1600576714027782 The application of small-angle X-ray scattering (SAXS) for high-throughput characterization of biological macromolecules in solution is limited by radiation damage. By cryocooling samples, radiation damage and required sample volumes can be reduced by …

  52. A multi-model approach to assessing local and global cryo-EM map quality

    0.0 out of 5 stars 

    20 Apr 2017 | BioXFEL Publications | Contributor(s): Mark A Herzik, James Fraser, Gabriel C Lander

    http://dx.doi.org/10.1101/128561 There does not currently exist a standardized indicator of how well a cryo-EM-derived model represents the density from which it was generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models …

  53. A New Approach to Signal Processing of Spatiotemporal Data

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    07 Sep 2018 | BioXFEL Publications | Contributor(s): Joanna Slawinska, Abbas Ourmazd, Dimitrios Giannakis

    http://dx.doi.org/10.1109/ssp.2018.8450704 proceedings-article Slawinska, J., Ourmazd, A. & Giannakis, D., 2018. A New Approach to Signal Processing of Spatiotemporal Data. 2018 IEEE Statistical Signal Processing Workshop (SSP). Available at: http://dx.doi.org/10.1109/ssp.2018.8450704. Joanna …

  54. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy

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    22 Feb 2021 | BioXFEL Publications | Contributor(s): J.P.J. Chen, K.E. Schmidt, J.C.H. Spence, R.A. Kirian

    http://dx.doi.org/10.1016/j.ultramic.2021.113234 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Chen, J.P.J. et al., 2021. A new solution to the curved Ewald sphere problem for 3D image reconstruction in electron microscopy. Ultramicroscopy, p.113234. Available at: …

  55. A new view on crystal harvesting

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    28 May 2014 | BioXFEL Publications | Contributor(s): Joseph Luft, Thomas D. Grant, Jennifer R. Wolfley, Edward Snell

    X-ray crystallography typically requires the mounting of crystals, which can make the sample difficult to manipulate when it is small and the microscope objective is close to the crystallization plate. By simply moving the objective to the bottom of a clear crystallization plate (inverting the …

  56. A novel form of allosteric regulation in Bacillus subtilis ribonucleotide reductase revealed by SAXS and cryo-electron microscopy

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    05 Feb 2019 | BioXFEL Publications | Contributor(s): William C. Thomas, Frederick P. Brooks, Mackenzie J. Parker, David Case, Jason T. Kaelber, JoAnne Stubbe, James Chen, Nozomi Ando

    http://dx.doi.org/10.1107/s0108767318099142 journal-article Thomas, W. C., Brooks, F. P., Parker, M. J., Case, D. A., Kaelber, J. T., Stubbe, J., Chen, J., & Ando, N. (2018). A novel form of allosteric regulation in Bacillus subtilis ribonucleotide reductase revealed by SAXS and cryo-electron …

  57. A novel inert crystal delivery medium for serial femtosecond crystallography

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    29 Jun 2015 | BioXFEL Publications | Contributor(s): Chelsie E Conrad, Shibom Basu, Daniel James, Dingjie Wang, Alexander Schaffer, Shatabdi Roy-Chowdhury, Nadia Zatsepin, Andrew Aquila, Jesse David Coe, Cornelius Gati, Mark S. Hunter, Jason E. Koglin, Christopher Kupitz, Garrett Charles Nelson, GANESH SUBRAMANIAN, Thomas A. White, Yun Zhao, James D Zook, Sébastien Boutet, Vadim Cherezov, John Spence, Raimund Fromme, Uwe Weierstall, Petra Fromme

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from …

  58. A peak-finding algorithm based on robust statistical analysis in serial crystallography

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    03 Nov 2017 | BioXFEL Publications | Contributor(s): Marjan Hadian-Jazi, Marc Messerschmidt, Connie Darmanin, Klaus Giewekemeyer, Adrian P. Mancuso, Brian Abbey

    http://dx.doi.org/10.1107/s1600576717014340 The recent development of serial crystallography at synchrotron and X-ray free-electron laser (XFEL) sources is producing crystallographic datasets of ever increasing volume. The size of these datasets is such that fast and efficient analysis presents a …

  59. A Remarkable Return On Investment In Fundamental Research: 40 Years of Basic Energy Sciences at the Department of Energy

    0.0 out of 5 stars 

    02 Aug 2019 | BioXFEL Publications | Contributor(s): Persis Drell, Dawn A. Bonnell, Jingguang Chen, Sue Clark, Beatriz Roldan Cuenya, Helmut Dosch, Cynthia Friend, Yan Gao, Sharon Hammes-Schiffer, Marc Kastner, Bruce Kay, Stephen R. Leone, Despina Louca, Monica Olvera De La Cruz, Abbas Ourmazd, Philippe Piot, Ian Robertson, Anthony Rollett, Frances Ross, Gary Rubloff, Maria Santore, Esther S. Takeuchi, John Tranquada, Stephen Wasserman

    http://dx.doi.org/10.2172/1545686 report Drell, P. et al., 2018. A Remarkable Return On Investment In Fundamental Research: 40 Years of Basic Energy Sciences at the Department of Energy. Available at: http://dx.doi.org/10.2172/1545686. Persis Drell and Dawn A. Bonnell and Jingguang Chen and Sue …

  60. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

    0.0 out of 5 stars 

    30 Apr 2020 | BioXFEL Publications | Contributor(s): David E. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M. White, Matthew J. O’Meara, Veronica V. Rezelj, Jeffrey Z. Guo, Danielle L. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia L. Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T. Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong A. Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J. P. Mathy, Tina Perica, Kala Bharath Pilla, Sai J. Ganesan, Daniel J. Saltzberg, Ramachandran Rakesh, Xi Liu, Sara B. Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, Jose Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A. Wankowicz, Markus Bohn, Maliheh Safari, Fatima S. Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J. Fletcher, Michael C. O’Neal, Yiming Cai, Jason C. J. Chang, David J. Broadhurst, Saker Klippsten, Phillip P. Sharp, Nicole A. Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M. Young, Devin A. Cavero, Joseph Hiatt, Theodore L. Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert Stroud, Alan D. Frankel, Oren S. Rosenberg, Kliment A. Verba, David A. Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark Von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe D’Enfert, Shaeri Mukherjee, Matt Jacobson, Harmit S. Malik, Danica G. Fujimori, Trey Ideker, Charles S. Craik, Stephen N. Floor, James Fraser, John D. Gross, Andrej Sali, Bryan L. Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo García-Sastre, Kevan M. Shokat, Brian K. Shoichet, Nevan J. Krogan

    http://dx.doi.org/10.1038/s41586-020-2286-9 journal-article Gordon, D.E. et al., 2020. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), pp.459–468. Available at: http://dx.doi.org/10.1038/s41586-020-2286-9. David E. Gordon and Gwendolyn M. Jang and …

  61. A SAXS-based approach to rationally evaluate radical scavengers – toward eliminating radiation damage in solution and crystallographic studies

    0.0 out of 5 stars 

    10 Aug 2021 | BioXFEL Publications | Contributor(s): Timothy R. Stachowski, Mary E. Snell, Edward Snell

    http://dx.doi.org/10.1107/s1600577521004045 X-ray-based techniques are a powerful tool in structural biology but the radiation-induced chemistry that results can be detrimental and may mask an accurate structural understanding. In the crystallographic case, cryocooling has been employed as a …

  62. A scalable lysyl hydroxylase 2 expression system and luciferase-based enzymatic activity assay

    0.0 out of 5 stars 

    21 Feb 2017 | BioXFEL Publications | Contributor(s): Hou-Fu Guo, Eun Jeong Cho, Ashwini K. Devkota, Yulong Chen, William Russell, George Phillips, Mitsuo Yamauchi, Kevin N. Dalby, Jonathan M. Kurie

    journal-article http://dx.doi.org/10.1016/j.abb.2017.02.003 Guo, H.-F. et al., 2017. A scalable lysyl hydroxylase 2 expression system and luciferase-based enzymatic activity assay. Archives of Biochemistry and Biophysics, 618, pp.45–51. Available at: http://dx.doi.org/10.1016/j.abb.2017.02.003. …

  63. A science education model for large collaborative centers

    0.0 out of 5 stars 

    05 Mar 2021 | BioXFEL Publications | Contributor(s): William J. Bauer, Sarah Woodruff

    http://dx.doi.org/10.1063/4.0000081 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Bauer, W.J. & Woodruff, S.B., 2021. A science education model for large collaborative centers. Structural Dynamics, 8(2), p.020402. Available at: http://dx.doi.org/10.1063/4.0000081. William J. …

  64. A short history of structure based research on the photocycle of photoactive yellow protein

    0.0 out of 5 stars 

    31 Jan 2017 | BioXFEL Publications | Contributor(s): Marius Schmidt

    journal-article http://dx.doi.org/10.1063/1.4974172 NSF-STC Biology with X-ray Lasers (NSF-1231306) Schmidt, M., 2017. A short history of structure based research on the photocycle of photoactive yellow protein. Structural Dynamics, 4(3), p.032201. Available at: …

  65. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo

    0.0 out of 5 stars 

    31 Aug 2023 | BioXFEL Publications | Contributor(s): Taha Y. Taha, Rahul K. Suryawanshi, Irene P. Chen, Galen J. Correy, Maria McCavitt-Malvido, Patrick C. O’Leary, Manasi P. Jogalekar, Morgan E. Diolaiti, Gabriella R. Kimmerly, Chia-Lin Tsou, Ronnie Gascon, Mauricio Montano, Luis Martinez-Sobrido, Nevan J. Krogan, Alan Ashworth, James Fraser, Melanie Ott

    http://dx.doi.org/10.1371/journal.ppat.1011614 Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 …

  66. A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine

    0.0 out of 5 stars 

    13 Jan 2020 | BioXFEL Publications | Contributor(s): Sweta Vangaveti, William A. Cantara, Jessica L. Spears, Hasan Demirci, Frank V. Murphy, Sri V. Ranganathan, Kathryn L. Sarachan, Paul F. Agris

    http://dx.doi.org/10.1016/j.jmb.2019.12.016 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Vangaveti, S. et al., 2020. A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. Journal of Molecular Biology, 432(4), …

  67. A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation

    0.0 out of 5 stars 

    16 Jan 2014 | BioXFEL Publications | Contributor(s): Kevin K. Desai, Chin L. Cheng, Craig A. Bingman, George Phillips, Ronald T. Raines

    http://dx.doi.org/10.1093/nar/gkt1375 journal-article Desai, K.K. et al., 2014. A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation. Nucleic Acids Research, 42(6), pp.3931–3942. Available at: http://dx.doi.org/10.1093/nar/gkt1375. …

  68. A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin

    0.0 out of 5 stars 

    07 Sep 2023 | BioXFEL Publications | Contributor(s): Do-Hyun Kim, Yilin Wang, Haerin Jung, Rachael L. Field, Xinya Zhang, Ta-Chiang Liu, Changqing Ma, James Fraser, Jonathan R. Brestoff, Steven J. Van Dyken

    http://dx.doi.org/10.1126/science.add5649 Dietary fiber improves metabolic health, but host-encoded mechanisms for digesting fibrous polysaccharides are unclear. In this work, we describe a mammalian adaptation to dietary chitin that is coordinated by gastric innate immune activation and acidic …

  69. A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography

    0.0 out of 5 stars 

    25 Sep 2023 | BioXFEL Publications | Contributor(s): Zhongrui Liu, Kevin Gu, Megan Shelby, Deepshika Gilbile, Artem Y. Lyubimov, Silvia Russi, Aina E. Cohen, Sankar Raju Narayanasamy, Sabine Botha, Christopher Kupitz, Raymond G. Sierra, Fredric Poitevin, Antonio Gilardi, Stella Lisova, Matthew Coleman, Matthias Frank, Tonya L. Kuhl

    http://dx.doi.org/10.1107/s2059798323007027 Over the past two decades, serial X-ray crystallography has enabled the structure determination of a wide range of proteins. With the advent of X-ray free-electron lasers (XFELs), ever-smaller crystals have yielded high-resolution diffraction and …

  70. Ab initio electron density determination directly from solution scattering data

    0.0 out of 5 stars 

    29 Jan 2018 | BioXFEL Publications | Contributor(s): Thomas D Grant

    http://dx.doi.org/10.1038/nmeth.4581 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Grant, T.D., 2018. Ab initio electron density determination directly from solution scattering data. Nature Methods. Available at: http://dx.doi.org/10.1038/nmeth.4581. Thomas D Grant

  71. Ab initio phasing of the diffraction of crystals with translational disorder

    0.0 out of 5 stars 

    20 Dec 2018 | BioXFEL Publications | Contributor(s): Andrew J. Morgan, Kartik Ayyer, Anton Barty, Joe Chen, Tomas Ekeberg, Dominik Oberthuer, Thomas A. White, Oleksandr Yefanov, Henry Chapman

    http://dx.doi.org/10.1107/s2053273318015395 To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined …

  72. Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

    0.0 out of 5 stars 

    01 Oct 2013 | BioXFEL Publications | Contributor(s): Haiguang Liu, Nadia Zatsepin, John Spence

    X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that …

  73. Ab-initio phasing using nanocrystal shape transforms with incomplete unit cells

    0.0 out of 5 stars 

    13 Oct 2015 | Teaching Materials

    X-ray free electron lasers are used in measuring diffraction patterns from nanocrystals in the `diffract-before-destroy' mode by outrunning radiation damage. The finite-sized nanocrystals provide an opportunity to recover intensity between Bragg spots by removing the modulating function that …

  74. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source

    0.0 out of 5 stars 

    25 Aug 2014 | BioXFEL Publications | Contributor(s): K. Tiedtke, A. A. Sorokin, U. Jastrow, P. Juranić, S. Kreis, N. Gerken, M. Richter, U. Arp, Y. Feng, D. Nordlund, R. Soufli, M. Fernández-Perea, L. Juha, P. Heimann, B. Nagler, H. J. Lee, S. Mack, M. Cammarata, O. Krupin, M. Messerschmidt, M. Holmes, M. Rowen, W. Schlotter, S. Moeller, J. J. Turner

    journal-article http://dx.doi.org/10.1364/oe.22.021214 Tiedtke, K. et al., 2014. Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source. Optics Express, 22(18), p.21214. Available at: http://dx.doi.org/10.1364/oe.22.021214. K. Tiedtke and A. A. Sorokin and U. Jastrow …

  75. Abstract 13747: Targeting Urokinase-Type Plasminogen Activator (uPA) and the uPA Receptor, Reduces Vascular Inflammation and Lung Hemorrhage in Systemic Lupus and SARS CoV2 Infection in Mouse Models of Respiratory Distress Syndromes

    0.0 out of 5 stars 

    16 Dec 2021 | BioXFEL Publications | Contributor(s): Liqiang Zhang, Jordan R Yaron, Lauren Schutz, Emily Aliskevich, Kyle Browder, Nicholas Saldevar, Isabela R Zanetti, Nora Elmadbouly, Honor Glenn, Yize Li, Karen Kibler, Brenda Hogue, Grant McFadden, Alexandra R Lucas

    http://dx.doi.org/10.1161/circ.144.suppl_2.13747 Introduction: Acute respiratory distress syndromes with vascular inflammation and alveolar hemorrhage have high mortality and limited treatment. Autoimmune disease and severe viral infection cause vascular inflammation and …

  76. Abstract 1473 Integrating Machine Learning and Functional Genomics to Prioritize CVD-associated Mutations Altering NKX2-5 and TBX5 DNA Binding

    0.0 out of 5 stars 

    25 Mar 2024 | BioXFEL Publications | Contributor(s): Edwin Peña-Martínez, Diego Pomales-Matos, Alejandro Rivera-Madera, Jean Messon-Bird, Joshua Medina-Feliciano, Leandro Sanabria-Alberto, Adriana Barreiro-Rosario, Jeancarlos Rivera-Del Valle, Jose Arcadio Rodriguez-Martinez

    http://dx.doi.org/10.1016/j.jbc.2024.106540 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Peña-Martínez, E., Pomales-Matos, D., Rivera-Madera, A., Messon-Bird, J., Medina-Feliciano, J., Sanabria-Alberto, L., Barreiro-Rosario, A., Rivera-Del Valle, J., & Rodríguez-Martínez, J. …

  77. Abstract 2307 Evaluating the thermal stability of congenital heart diseases-associated TBX5 missense mutants

    0.0 out of 5 stars 

    25 Mar 2024 | BioXFEL Publications | Contributor(s): Alejandro Rivera-Madera, Edwin Peña-Martínez, Jose Arcadio Rodriguez-Martinez

    http://dx.doi.org/10.1016/j.jbc.2024.107071 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Rivera-Madera, A., Peña-Martínez, E., & Rodriguez-Martinez, J. (2024). Abstract 2307 Evaluating the thermal stability of congenital heart diseases-associated TBX5 missense mutants. Journal …

  78. Abstract P6-19-01: Evaluation of multiple transcriptomic gene risk signatures in male breast cancer

    0.0 out of 5 stars 

    11 May 2019 | BioXFEL Publications | Contributor(s): J Bayani, C Poncet, CQ Yao, C Crozier, N Anouk, T Piper, C Cunningham, M Sobol, S Aebi, K Benstead, O Bogler, L Dal Lago, J Fraser, FH Hilbers, I Hedenfalk, L Korde, B Linderholm, J Martens, L Middleton, M Murray, C Kelly, C Nilsson, M Nowaczyk, S Peeters, A Peric, P Porter, C Schröder, IT Rubio, KJ Ruddy, C Van Asperen, D Van Den Weyngaert, C Van Deurzen, E Van Leeuwen-Stok, J Vermeij, E Winer, PC Boutros, SH Giordano, F Cardoso, JM Bartlett

    http://dx.doi.org/10.1158/1538-7445.sabcs18-p6-19-01 proceedings-article Bayani, J. et al., 2019. Abstract P6-19-01: Evaluation of multiple transcriptomic gene risk signatures in male breast cancer. Poster Session Abstracts. Available at: http://dx.doi.org/10.1158/1538-7445.sabcs18-p6-19-01. J …

  79. Accurate determination of segmented X-ray detector geometry

    0.0 out of 5 stars 

    22 Oct 2015 | BioXFEL Publications | Contributor(s): Oleksandr Yefanov, Valerio Mariani, Cornelius Gati, Thomas A. White, Henry Chapman, Anton Barty

    http://dx.doi.org/10.1364/oe.23.028459 Oleksandr Yefanov and Valerio Mariani and Cornelius Gati and Thomas A. White and Henry N. Chapman and Anton Barty Yefanov, O. et al., 2015. Accurate determination of segmented X-ray detector geometry. Optics Express, 23(22), p.28459. Available at: …

  80. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    0.0 out of 5 stars 

    16 Mar 2014 | BioXFEL Publications | Contributor(s): Johan Hattne, Nathaniel Echols, Rosalie Tran, Jan Kern, Richard J Gildea, Aaron S Brewster, Roberto Alonso-Mori, Carina Glöckner, Julia Hellmich, Hartawan Laksmono, Raymond G Sierra, Benedikt Lassalle-Kaiser, Alyssa Lampe, Guangye Han, Sheraz Gul, Dörte DiFiore, Despina Milathianaki, Alan R Fry, Alan Miahnahri, William E White, Donald W Schafer, M Marvin Seibert, Jason E Koglin, Dimosthenis Sokaras, Tsu-Chien Weng, Jonas Sellberg, Matthew J Latimer, Pieter Glatzel, Petrus H Zwart, Ralf W Grosse-Kunstleve, Michael J Bogan, Marc Messerschmidt, Garth J Williams, Sébastien Boutet, Johannes Messinger, Athina Zouni, Junko Yano, Uwe Bergmann, Vittal K Yachandra, Paul D Adams, Nicholas K Sauter

    journal-article http://dx.doi.org/10.1038/nmeth.2887 Hattne, J. et al., 2014. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods, 11(5), pp.545–548. Available at: http://dx.doi.org/10.1038/nmeth.2887. Johan Hattne and Nathaniel Echols …

  81. Accurate positioning of functional residues with robotics-inspired computational protein design

    0.0 out of 5 stars 

    07 Mar 2022 | BioXFEL Publications | Contributor(s): Cody Krivacic, Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane O Conchúir, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Michael Thompson, James Fraser, Tanja Kortemme

    http://dx.doi.org/10.1073/pnas.2115480119 Significance Computational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level …

  82. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

    0.0 out of 5 stars 

    29 Sep 2014 | BioXFEL Publications | Contributor(s): Hung T. Nguyen, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack, David Case

    http://dx.doi.org/10.1063/1.4896220 journal-article Nguyen, H.T. et al., 2014. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. The Journal of Chemical Physics, 141(22), p.22D508. Available at: http://dx.doi.org/10.1063/1.4896220. Hung T. …

  83. Advanced Transmission Electron Microscopy

    0.0 out of 5 stars 

    25 Oct 2016 | BioXFEL Publications | Contributor(s): Jian Min Zuo, John Spence

    http://dx.doi.org/10.1007/978-1-4939-6607-3 book Zuo, J.M. & Spence, J.C.H., 2017. Advanced Transmission Electron Microscopy. Available at: http://dx.doi.org/10.1007/978-1-4939-6607-3. Jian Min Zuo and John C.H. Spence

  84. Advances in methods for atomic resolution macromolecular structure determination

    0.0 out of 5 stars 

    02 Jul 2020 | BioXFEL Publications | Contributor(s): Michael Thompson, Todd O. Yeates, Jose A. Rodriguez

    http://dx.doi.org/10.12688/f1000research.25097.1 Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. …

  85. Advances in Structure Determination of G Protein-Coupled Receptors by SFX

    0.0 out of 5 stars 

    27 Dec 2018 | BioXFEL Publications | Contributor(s): Benjamin Stauch, Linda Johansson, Andrii Ishchenko, Gye Won Han, Alexander Batyuk, Vadim Cherezov

    http://dx.doi.org/10.1007/978-3-030-00551-1_10 book-chapter Stauch, B. et al., 2018. Advances in Structure Determination of G Protein-Coupled Receptors by SFX. X-ray Free Electron Lasers, pp.301–329. Available at: http://dx.doi.org/10.1007/978-3-030-00551-1_10. Benjamin Stauch and Linda …

  86. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex

    0.0 out of 5 stars 

    12 Oct 2016 | BioXFEL Publications | Contributor(s): Artem Y Lyubimov, Monarin Uervirojnangkoorn, Oliver B Zeldin, Qiangjun Zhou, Minglei Zhao, Aaron S Brewster, Tara Michels-Clark, James Holton, Nicholas K Sauter, William I Weis, Axel T Brunger

    X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited …

  87. Algorithm for Reconstruction of 3D Images of Nanorice Particles from Diffraction Patterns of Two Particles in Independent Random Orientations with an X-ray Laser

    0.0 out of 5 stars 

    23 Jun 2017 | BioXFEL Publications | Contributor(s): Sung Soon Kim, Sandi Wibowo, Dilano Saldin

    http://dx.doi.org/10.3390/app7070646 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) Kim, S., Wibowo, S. & Saldin, D., 2017. Algorithm for Reconstruction of 3D Images of Nanorice Particles from Diffraction Patterns of Two Particles in Independent Random Orientations with an X-ray …

  88. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations

    0.0 out of 5 stars 

    06 Mar 2013 | BioXFEL Publications | Contributor(s): Michael D. Daily, Haibo Yu, George Phillips, Qiang Cui

    http://dx.doi.org/10.1007/128_2012_409 book-chapter Daily, M.D. et al., 2013. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Topics in Current Chemistry, pp.139–164. Available at: …

  89. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases

    0.0 out of 5 stars 

    31 Jul 2017 | BioXFEL Publications | Contributor(s): Timothy M. Acker, Jonathan E. Gable, Markus-Frederik Bohn, Priyadarshini Jaishankar, Michael Thompson, James Fraser, Adam R. Renslo, Charles S. Craik

    http://dx.doi.org/10.1021/jacs.7b04030 journal-article Acker, T.M. et al., 2017. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. Journal of the American Chemical Society. Available at: …

  90. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature

    0.0 out of 5 stars 

    19 Jul 2018 | BioXFEL Publications | Contributor(s): Mary E. O'Sullivan, Frederic Poitevin, Raymond G. Sierra, Cornelius Gati, E. Han Dao, Yashas Rao, Fulya Aksit, Halilibrahim Ciftci, Nicholas Corsepius, Robert Greenhouse, Brandon Hayes, Mark S. Hunter, Mengling Liang, Alex McGurk, Paul Mbgam, Trevor Obrinsky, Fatima Pardo-Avila, Matt Seaberg, Alan G. Cheng, Anthony J. Ricci, Hasan Demirci

    http://dx.doi.org/10.1101/372144 The bacterial 30S ribosomal subunit is a primary antibiotic target. Despite decades of discovery, the mechanisms by which antibiotic binding induces ribosomal dysfunction are not fully understood. Ambient temperature crystallographic techniques allow more …

  91. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature

    0.0 out of 5 stars 

    20 Jul 2018 | BioXFEL Publications | Contributor(s): Mary E O’Sullivan, Frédéric Poitevin, Raymond G Sierra, Cornelius Gati, E Han Dao, Yashas Rao, Fulya Aksit, Halilibrahim Ciftci, Nicholas Corsepius, Robert Greenhouse, Brandon Hayes, Mark S Hunter, Mengling Liang, Alex McGurk, Paul Mbgam, Trevor Obrinsky, Fátima Pardo-Avila, Matthew H Seaberg, Alan G Cheng, Anthony J Ricci, Hasan Demirci

    http://dx.doi.org/10.1093/nar/gky693 journal-article NSF-STC Biology with X-ray Lasers (NSF-1231306) O’Sullivan, M.E. et al., 2018. Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature. Nucleic Acids Research, 46(18), pp.9793–9804. Available at: …

  92. Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry

    0.0 out of 5 stars 

    15 Mar 2022 | BioXFEL Publications | Contributor(s): Jorvani Cruz Villarreal, Ana Egatz‐Gomez, Jiawei Liu, Robert Ros, George T. Noutsios, Todd R. Sandrin, Paul D. Coleman, Alexandra Ros

    http://dx.doi.org/10.1002/alz.054274 journal-article Villarreal, J. C., Egatz‐Gomez, A., Liu, J., Ros, R., Noutsios, G. T., Sandrin, T. R., Coleman, P. D., & Ros, A. (2021). Amyloid‐β analysis from brain cells using microfluidics and mass spectrometry. Alzheimer’s & Dementia, 17(S3). …

  93. An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

    0.0 out of 5 stars 

    22 Apr 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

    http://dx.doi.org/10.1101/2020.04.17.20069641 On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona of an individual with travel history (3rd case in the US) (1). Here, we report on early SARS-CoV-2 sentinel surveillance in Tempe, Arizona (USA). Genomic …

  94. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

    0.0 out of 5 stars 

    01 May 2020 | BioXFEL Publications | Contributor(s): LaRinda A. Holland, Emily A. Kaelin, Rabia Maqsood, Bereket Estifanos, Lily I. Wu, Arvind Varsani, Rolf U. Halden, Brenda Hogue, Matthew Scotch, Efrem S. Lim

    http://dx.doi.org/10.1128/jvi.00711-20 journal-article Holland, L.A. et al., 2020. An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020) T. Gallagher, ed. Journal of Virology, 94(14). Available at: …

  95. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser

    0.0 out of 5 stars 

    15 Oct 2020 | BioXFEL Publications | Contributor(s): Dameli Assalauova, Young Yong Kim, Sergey Bobkov, Ruslan Khubbutdinov, Max Rose, Roberto Alvarez, Jakob Andreasson, Eugeniu Balaur, Alice Contreras, Hasan Demirci, Luca Gelisio, Janos Hajdu, Mark S. Hunter, Ruslan P. Kurta, Haoyuan Li, Matthew McFadden, Reza Nazari, Peter Schwander, Anton Teslyuk, Peter Walter, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare, Viacheslav A. Ilyin, Richard Kirian, Brenda Hogue, Andrew Aquila, Ivan A. Vartanyants

    http://dx.doi.org/10.1107/s2052252520012798 An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent …

  96. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. Corrigendum

    0.0 out of 5 stars 

    24 Jan 2022 | BioXFEL Publications | Contributor(s): Dameli Assalauova, Young Yong Kim, Sergey Bobkov, Ruslan Khubbutdinov, Max Rose, Roberto Alvarez, Jakob Andreasson, Eugeniu Balaur, Alice Contreras, Hasan Demirci, Luca Gelisio, Janos Hajdu, Mark S. Hunter, Ruslan P. Kurta, Haoyuan Li, Matthew McFadden, Reza Nazari, Peter Schwander, Anton Teslyuk, Peter Walter, P. Lourdu Xavier, Chun Hong Yoon, Sahba Zaare, Viacheslav A. Ilyin, Richard Kirian, Brenda Hogue, Andrew Aquila, Ivan A. Vartanyants

    http://dx.doi.org/10.1107/s2052252522000501 An error in Fig. 3(c) of the article by Assalauova et al. [IUCrJ (2020), 7, 1102–1113] is corrected. journal-article Assalauova, D., Kim, Y. Y., Bobkov, S., Khubbutdinov, R., Rose, M., Alvarez, R., Andreasson, J., Balaur, E., Contreras, A., DeMirci, …

  97. An Engineered TGF-β Monomer that Functions as a Dominant Negative to Block TGF-β Signaling

    0.0 out of 5 stars 

    22 Feb 2017 | BioXFEL Publications | Contributor(s): Sun Kyung Kim, Lindsey Barron, Cynthia S. Hinck, Elyse M. Petrunak, Kristin E. Cano, Avinash Thangirala, Brian Iskra, Molly Brothers, Machell Vonberg, Belinda Leal, Blair Richter, Ravindra Kodali, Alexander B. Taylor, Shoucheng Du, Christopher Barnes, Traian Sulea, Guillermo Calero, P. John Hart, Matthew J. Hart, Borries Demeler, Andrew P. Hinck

    journal-article http://dx.doi.org/10.1074/jbc.m116.768754 Kim, S.K. et al., 2017. An Engineered TGF-β Monomer that Functions as a Dominant Negative to Block TGF-β Signaling. Journal of Biological Chemistry, p.jbc.M116.768754. Available at: http://dx.doi.org/10.1074/jbc.m116.768754. Sun Kyung …

  98. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

    0.0 out of 5 stars 

    06 Jun 2018 | BioXFEL Publications | Contributor(s): Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T Justin Rettenmaier, José Brandão-Neto, Nicholas M Pearce, Frank Von Delft, James A Wells, James Fraser

    http://dx.doi.org/10.7554/elife.36307 Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we …

  99. An Extension of 3D Zernike Moments for Shape Description and Retrieval of Maps Defined in Rectangular Solids

    0.0 out of 5 stars 

    23 Apr 2013 | BioXFEL Publications | Contributor(s): Atilla Sit, Julie C Mitchell, George Phillips, Stephen J Wright

    http://dx.doi.org/10.2478/mlbmb-2013-0004 journal-article Sit, A. et al., 2013. An Extension of 3D Zernike Moments for Shape Description and Retrieval of Maps Defined in Rectangular Solids. Molecular Based Mathematical Biology, 1. Available at: http://dx.doi.org/10.2478/mlbmb-2013-0004. Atilla …

  100. An in Vitro Investigation of Globin Folding and Expression

    0.0 out of 5 stars 

    16 Feb 2016 | BioXFEL Publications | Contributor(s): Premila P. Samuel, William Ou, George Phillips, John S. Olson

    http://dx.doi.org/10.1016/j.bpj.2015.11.1166 journal-article Samuel, P.P. et al., 2016. An in Vitro Investigation of Globin Folding and Expression. Biophysical Journal, 110(3), p.209a–210a. Available at: http://dx.doi.org/10.1016/j.bpj.2015.11.1166. Premila P. Samuel and William Ou and George …

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