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  • Improved AlphaFold modeling with implicit experimental information. 

    Terwilliger, Thomas C; Poon, Billy K; Afonine, Pavel V; Schlicksup, Christopher J; Croll, Tristan I; Millán, Claudia; Richardson, Jane S; ... (9 authors) (Nature methods, 2022-11)
    Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. ...
  • Accelerating crystal structure determination with iterative AlphaFold prediction. 

    Terwilliger, Thomas C; Afonine, Pavel V; Liebschner, Dorothee; Croll, Tristan I; McCoy, Airlie J; Oeffner, Robert D; Williams, Christopher J; ... (11 authors) (Acta crystallographica. Section D, Structural biology, 2023-03)
    Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold. Here, an automatic procedure requiring only sequence information and crystallographic ...
  • The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. 

    Williams, Christopher J; Richardson, David C; Richardson, Jane S (Protein science : a publication of the Protein Society, 2022-01)
    We have curated a high-quality, "best-parts" reference dataset of about 3 million protein residues in about 15,000 PDB-format coordinate files, each containing only residues with good electron density support for a physically ...
  • Metabolic factors associated with incident fracture among older adults with type 2 diabetes mellitus: a nested case-control study. 

    Lee, Richard H; Bain, James; Muehlbauer, Michael; Ilkayeva, Olga; Pieper, Carl; Wixted, Doug; Colón-Emeric, Cathleen (Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA, 2023-07)
    Older adults with type 2 diabetes mellitus have an increased risk of fracture despite a paradoxically higher average bone mineral density. This study identified additional markers of fracture risk in this at-risk population. ...
  • Nightshift imposes irregular lifestyle behaviors in police academy trainees. 

    Erickson, Melissa L; North, Rebecca; Counts, Julie; Wang, Will; Porter Starr, Kathryn N; Wideman, Laurie; Pieper, Carl; ... (9 authors) (Sleep advances : a journal of the Sleep Research Society, 2023-01)
    <h4>Study objective</h4>Shiftwork increases risk for numerous chronic diseases, which is hypothesized to be linked to disruption of circadian timing of lifestyle behaviors. However, empirical data on timing of lifestyle ...

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