# Publications Search Within Results Search Within Results search ## 15 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 15 results Download 15 citations download- [BibTeX](/node/1851456/export?format=bibtex) - [EndNote X3 XML](/node/1851456/export?format=endnote8) - [EndNote 7 XML](/node/1851456/export?format=endnote7) - [Endnote tagged](/node/1851456/export?format=tagged) - [Marc](/node/1851456/export?format=marc) - [PubMedId](/node/1851456/export?format=pubmed_id) - [RIS](/node/1851456/export?format=ris) ### 2024 Jack B. Greisman, Kevin M. Dalton, Dennis E. Brookner, Margaret A. Klureza, Candice J. Sheehan, In-Sik Kim, Robert W. Henning, Silvia Russi, and Doeke R. Hekstra. 2024. “[Perturbative Diffraction Methods Resolve a Conformational Switch That Facilitates a Two-Step Enzymatic Mechanism](/publications/resolving-conformational-changes-mediate-two-step-catalytic-mechanism-model)”. PNAS, 121, 9. doi:10.1101/2023.06.02.543507 Jack B. Greisman, Kevin M. Dalton, Dennis E. Brookner, Margaret A. Klureza, Candice J. Sheehan, In-Sik Kim, Robert W. Henning, Silvia Russi, and Doeke R. Hekstra. 2024. “[Perturbative Diffraction Methods Resolve a Conformational Switch That Facilitates a Two-Step Enzymatic Mechanism](/publications/resolving-conformational-changes-mediate-two-step-catalytic-mechanism-model)”. PNAS, 121, 9. doi:10.1101/2023.06.02.543507 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2313192121) Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to poor experimental... - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2313192121) Dennis E. Brookner and Doeke R. Hekstra. 2024. “[MatchMaps: Non-Isomorphous Difference Maps for X-Ray Crystallography](/publications/matchmaps-non-isomorphous-difference-maps-x-ray-crystallography)”. Journal of Applied Crystallography, 57, 3. doi:10.1101/2023.09.01.555333 Dennis E. Brookner and Doeke R. Hekstra. 2024. “[MatchMaps: Non-Isomorphous Difference Maps for X-Ray Crystallography](/publications/matchmaps-non-isomorphous-difference-maps-x-ray-crystallography)”. Journal of Applied Crystallography, 57, 3. doi:10.1101/2023.09.01.555333 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://journals.iucr.org/j/issues/2024/03/00/ei5112/index.html) Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands and time. A popular method for detecting structural... - [ descriptionPublisher's Version](https://journals.iucr.org/j/issues/2024/03/00/ei5112/index.html) Ian Hunt-Isaak, John Russell, and Doeke Hekstra. 2024. “[Mpl-Interactions: A Python Package for Interactive Matplotlib Figures](/publications/mpl-interactions-python-package-interactive-matplotlib-figures)”. Journal of Open Source Software Ian Hunt-Isaak, John Russell, and Doeke Hekstra. 2024. “[Mpl-Interactions: A Python Package for Interactive Matplotlib Figures](/publications/mpl-interactions-python-package-interactive-matplotlib-figures)”. Journal of Open Source Software - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://joss.theoj.org/papers/10.21105/joss.05651) Data exploration, model building and pedagogy all benefit from the ability to interactively update elements in Matplotlib (Hunter, 2007) figures. mpl-interactions enables this by making it easy for users to create Matplotlib figures in which the displayed... - [ descriptionPublisher's Version](https://joss.theoj.org/papers/10.21105/joss.05651) Rick A. Hewitt, Kevin M. Dalton, Derek Mendez, Harrison K. Wang, Margaret A. Klureza, Dennis E. Brookner, Jack B. Greisman, David McDonagh, Vukica \v Srajer, Nicholas K. Sauter, Aaron S. Brewster, and Doeke R. Hekstra. 2024. “[Laue-DIALS: Open-Source Software for Polychromatic X-Ray Diffraction Data](/publications/laue-dials-open-source-software-polychromatic-x-ray-diffraction-data)”. BioRxiv. doi:10.1101/2024.07.23.604358 Rick A. Hewitt, Kevin M. Dalton, Derek Mendez, Harrison K. Wang, Margaret A. Klureza, Dennis E. Brookner, Jack B. Greisman, David McDonagh, Vukica \v Srajer, Nicholas K. Sauter, Aaron S. Brewster, and Doeke R. Hekstra. 2024. “[Laue-DIALS: Open-Source Software for Polychromatic X-Ray Diffraction Data](/publications/laue-dials-open-source-software-polychromatic-x-ray-diffraction-data)”. BioRxiv. doi:10.1101/2024.07.23.604358 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/23/2024.07.23.604358) Most X-ray sources are inherently polychromatic. Polychromatic (“pink”) X-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/23/2024.07.23.604358) Doeke R. Hekstra, Harrison K. Wang, Margaret A. Klureza, Jack B. Greisman, and Kevin M. Dalton. 2024. “[Sensitive Detection of Structural Differences Using a Statistical Framework for Comparative Crystallography](/publications/sensitive-detection-structural-differences-using-statistical-framework)”. BioRxiv. doi:10.1101/2024.07.22.604476 Doeke R. Hekstra, Harrison K. Wang, Margaret A. Klureza, Jack B. Greisman, and Kevin M. Dalton. 2024. “[Sensitive Detection of Structural Differences Using a Statistical Framework for Comparative Crystallography](/publications/sensitive-detection-structural-differences-using-statistical-framework)”. BioRxiv. doi:10.1101/2024.07.22.604476 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/23/2024.07.22.604476) Chemical and conformational changes underlie the functional cycles of proteins. Comparative crystallography can reveal these changes over time, over ligands, and over chemical and physical perturbations in atomic detail. A key difficulty, however, is that... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/23/2024.07.22.604476) Ammaar A. Saeed, Margaret A. Klureza, and Doeke R. Hekstra. 2024. “[Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens](/publications/mapping-protein-conformational-landscapes-crystallographic-drug-fragment)”. BioRxiv. doi:10.1101/2024.07.29.605395 Ammaar A. Saeed, Margaret A. Klureza, and Doeke R. Hekstra. 2024. “[Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens](/publications/mapping-protein-conformational-landscapes-crystallographic-drug-fragment)”. BioRxiv. doi:10.1101/2024.07.29.605395 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/30/2024.07.29.605395) Proteins are dynamic macromolecules. Knowledge of a protein’s thermally accessible conformations is critical to determining important transitions and designing therapeutics. Accessible conformations are highly constrained by a protein’s structure such... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/30/2024.07.29.605395) Kara A. Zielinski, Cole Dolamore, Kevin M. Dalton, Nathan Smith, John Termini, Robert Henning, Vukica Srajer, Doeke R. Hekstra, Lois Pollack, and Mark A. Wilson. 2024. “[Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron](/publications/resolving-dj-1-glyoxalase-catalysis-using-mix-and-inject-serial)”. BioRxiv. doi:10.1101/2024.07.19.604369 Kara A. Zielinski, Cole Dolamore, Kevin M. Dalton, Nathan Smith, John Termini, Robert Henning, Vukica Srajer, Doeke R. Hekstra, Lois Pollack, and Mark A. Wilson. 2024. “[Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron](/publications/resolving-dj-1-glyoxalase-catalysis-using-mix-and-inject-serial)”. BioRxiv. doi:10.1101/2024.07.19.604369 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/20/2024.07.19.604369) DJ-1 (PARK7) is an intensively studied protein whose cytoprotective activities are dysregulated in multiple diseases. DJ-1 has been reported as having two distinct enzymatic activities in defense against reactive carbonyl species that are difficult to... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/20/2024.07.19.604369) Kara A. Zielinski, Cole Dolamore, Harrison K. Wang, Robert W. Henning, Mark A. Wilson, Lois Pollack, Vukica Srajer, Doeke R. Hekstra, and Kevin M. Dalton. 2024. “[Scaling and Merging Time-Resolved Laue Data With Variational Inference](/publications/scaling-and-merging-time-resolved-laue-data-variational-inference)”. BioRxiv. doi:10.1101/2024.07.30.605871 Kara A. Zielinski, Cole Dolamore, Harrison K. Wang, Robert W. Henning, Mark A. Wilson, Lois Pollack, Vukica Srajer, Doeke R. Hekstra, and Kevin M. Dalton. 2024. “[Scaling and Merging Time-Resolved Laue Data With Variational Inference](/publications/scaling-and-merging-time-resolved-laue-data-variational-inference)”. BioRxiv. doi:10.1101/2024.07.30.605871 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/31/2024.07.30.605871) Time-resolved X-ray crystallography (TR-X) at synchrotrons and free electron lasers is a promising technique for recording dynamics of molecules at atomic resolution. While experimental methods for TR-X have proliferated and matured, data analysis is... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/early/2024/07/31/2024.07.30.605871) ### 2023 Doeke R. Hekstra. 2023. “[Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics](/publications/emerging-time-resolved-x-ray-diffraction-approaches-protein-dynamics)”. Annual Review of Biophysics, 52, Pp. 255-74 Doeke R. Hekstra. 2023. “[Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics](/publications/emerging-time-resolved-x-ray-diffraction-approaches-protein-dynamics)”. Annual Review of Biophysics, 52, Pp. 255-74 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://doi.org/10.1146/annurev-biophys-111622-091155) Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles... - [ descriptionPublisher's Version](https://doi.org/10.1146/annurev-biophys-111622-091155) Luis A. Aldama, Kevin M. Dalton, and Doeke R. Hekstra. 2023. “[Correcting Systematic Errors in Diffraction Data With Modern Scaling Algorithms](/publications/correcting-systematic-errors-diffraction-data-modern-scaling-algorithms)”. Acta Crystallographica D, 79, 3, Pp. 796-805 Luis A. Aldama, Kevin M. Dalton, and Doeke R. Hekstra. 2023. “[Correcting Systematic Errors in Diffraction Data With Modern Scaling Algorithms](/publications/correcting-systematic-errors-diffraction-data-modern-scaling-algorithms)”. Acta Crystallographica D, 79, 3, Pp. 796-805 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://journals.iucr.org/d/issues/2023/09/00/qi5002/index.html) X-ray diffraction enables the routine determination of the atomic structure of materials. Key to its success are data-processing algorithms that allow experimenters to determine the electron density of a sample from its diffraction pattern. Scaling, the... - [ descriptionPublisher's Version](https://journals.iucr.org/d/issues/2023/09/00/qi5002/index.html) ### 2022 Jack B. Greisman, Kevin M. Dalton, Candice J. Sheehan, Margaret A. Klureza, Igor Kurinov, and Doeke R. Hekstra. 2022. “[Native SAD Phasing at Room Temperature](/publications/native-sad-phasing-room-temperature)”. Acta Crystallographica Section D, 78, 8. doi:10.1101/2021.12.13.472485 Jack B. Greisman, Kevin M. Dalton, Candice J. Sheehan, Margaret A. Klureza, Igor Kurinov, and Doeke R. Hekstra. 2022. “[Native SAD Phasing at Room Temperature](/publications/native-sad-phasing-room-temperature)”. Acta Crystallographica Section D, 78, 8. doi:10.1101/2021.12.13.472485 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://doi.org/10.1107/S2059798322006799) - [ picture\_as\_pdf2022greisman\_actad.pdf](/sites/g/files/omnuum7221/files/hekstralab/files/2022greisman_actad.pdf) Single-wavelength anomalous diffraction (SAD) is a routine method for overcoming the phase problem when solving macromolecular structures. This technique requires the accurate measurement of intensities to determine differences between Bijvoet pairs... - [ descriptionPublisher's Version](https://doi.org/10.1107/S2059798322006799) - [ picture\_as\_pdf2022greisman\_actad.pdf](/sites/g/files/omnuum7221/files/hekstralab/files/2022greisman_actad.pdf) Kevin Dalton, Jack Greisman, and Doeke Hekstra. 2022. “[A Unifying Bayesian Framework for Merging X-Ray Diffraction Data.](/publications/careless-variational-bayesian-model-merging-x-ray-diffraction-data-preprint)”. Nature Communications, 13. doi:10.1101/2021.01.05.425510 Kevin Dalton, Jack Greisman, and Doeke Hekstra. 2022. “[A Unifying Bayesian Framework for Merging X-Ray Diffraction Data.](/publications/careless-variational-bayesian-model-merging-x-ray-diffraction-data-preprint)”. Nature Communications, 13. doi:10.1101/2021.01.05.425510 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-022-35280-8) Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as... - [ descriptionPublisher's Version](https://www.nature.com/articles/s41467-022-35280-8) - Previous page chevron\_left - [1](?page=0 "Current page") - [2](?page=1 "Go to page 2") - [ Next page chevron\_right ](?page=1 "Go to next page")