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Showing 1–19 of 19 results
Advanced filters: Author: Abbas Ourmazd Clear advanced filters

  • The rise of machine learning is moving research away from tightly controlled, theory-guided experiments towards an approach based on data-driven searches. Abbas Ourmazd describes how this change might profoundly affect our understanding and practice of physics.

    • Abbas Ourmazd
    Comments & Opinion
    Nature Reviews Physics
    Volume: 2, P: 342-343

  • The opening mechanism of the SARS-CoV-2 spike protein has been studied by integrating computational and experimental data. Combining weighted ensemble molecular dynamics simulations, biolayer interferometry and ManifoldEM analysis of cryo-EM data revealed that the glycan at N343 plays a gating role in the opening mechanism of the SARS-CoV-2 spike protein.

    • Terra Sztain
    • Surl-Hee Ahn
    • Rommie E. Amaro
    Research
    Nature Chemistry
    Volume: 13, P: 963-968

  • An algorithm that reconstructs the structure of an object in flight from the diffraction pattern generated by exposing it to an ultrashort burst of X-rays should enhance the potential of free-electron lasers for studying individual molecules, virus and nanoparticles.

    • Russell Fung
    • Valentin Shneerson
    • Abbas Ourmazd
    Research
    Nature Physics
    Volume: 5, P: 64-67

  • Electron interferometry can be used to measure strain with nanoscale resolution in electronic devices by exploiting a simple idea found in physics textbooks.

    • Abbas Ourmazd
    News & Views
    Nature Nanotechnology
    Volume: 3, P: 381-382

  • There is a great interest in retrieving functional pathways from cryo-EM single-particle data. Here, the authors present an approach that combines cryo-EM with advanced data-analytical methods and molecular dynamics simulations to reveal the functional pathways traversed on experimentally derived energy landscapes using the ryanodine receptor type 1 as an example.

    • Ali Dashti
    • Ghoncheh Mashayekhi
    • Abbas Ourmazd
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14

  • The splendid computational success of AlphaFold and RoseTTAFold in solving the 60-year-old problem of protein folding raises an obvious question: what new avenues should structural biology explore? We propose a strong pivot toward the goal of reading mechanism and function directly from the amino acid sequence. This ambitious goal will require new data analytical tools and an extensive database of the atomic-level structural trajectories traced out on energy landscapes as proteins perform their function.

    • Abbas Ourmazd
    • Keith Moffat
    • Eaton Edward Lattman
    Comments & Opinion
    Nature Methods
    Volume: 19, P: 24-26

  • Here, the reaction of the suicide inhibitor sulbactam with the M. tuberculosis β-lactamase (BlaC) is investigated with time-resolved crystallography. Singular Value Decomposition is implemented to extract kinetic information despite changes in unit cell parameters during the time-course of the reaction.

    • Tek Narsingh Malla
    • Kara Zielinski
    • Marius Schmidt
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-15

  • The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.

    • Chris Gisriel
    • Jesse Coe
    • Nadia A. Zatsepin
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-11

  • Single-particle techniques offer an unprecedented opportunity to understand the role of structural variability in biological function. They also call into question the meaning of ‘a structure’ and its relevance to function.

    • Abbas Ourmazd
    Comments & Opinion
    Nature Methods
    Volume: 16, P: 941-944

  • Modern data science can help to address challenges in experimental chemistry. This Expert Recommendation describes examples of how data science is changing the way we conduct experiments and outlines opportunities for further integration of data science and experimental chemistry to advance these fields.

    • Junko Yano
    • Kelly J. Gaffney
    • Francesca M. Toma
    Reviews
    Nature Reviews Chemistry
    Volume: 6, P: 357-370

  • Diffractive imaging of single-particle nanoscale systems has so far been hindered by low hit probabilities and repetition rates. Here, single-particle imaging of nanospheres and viruses at megahertz repetition rates is demonstrated at the European X-ray Free-Electron Laser (XFEL) for the first time.

    • Egor Sobolev
    • Sergei Zolotarev
    • Filipe R. N. C. Maia
    ResearchOpen Access
    Communications Physics
    Volume: 3, P: 1-11