Publications by authors named "Frank DiMaio"

20Publications

Crystal Structure and Mechanistic Molecular Modeling Studies of Diterpene Cyclase Rv3377c.

Biochemistry 2020 Dec 12;59(47):4507-4515. Epub 2020 Nov 12.

Department of Chemistry, University of California-Davis, Davis, California 95616, United States.

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December 2020

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms.

Cell 2020 Oct 13;183(3):802-817.e24. Epub 2020 Oct 13.

Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address:

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October 2020

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination.

PLoS Comput Biol 2020 09 21;16(9):e1008103. Epub 2020 Sep 21.

Department of Biochemistry, University of Washington, Seattle, Washington, United States of America.

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September 2020

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM.

IUCrJ 2020 Sep 20;7(Pt 5):881-892. Epub 2020 Aug 20.

Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.

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September 2020

An enumerative algorithm for de novo design of proteins with diverse pocket structures.

Proc Natl Acad Sci U S A 2020 09 24;117(36):22135-22145. Epub 2020 Aug 24.

Institute for Protein Design, University of Washington, Seattle, WA 98195;

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September 2020

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.

Proc Natl Acad Sci U S A 2020 07 6;117(29):17003-17010. Epub 2020 Jul 6.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720;

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July 2020

The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation.

Nat Commun 2020 06 25;11(1):3210. Epub 2020 Jun 25.

Department of Molecular Biology and Biotechnology, the University of Sheffield, Sheffield, UK.

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June 2020

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Authors:
Julia Koehler Leman Brian D Weitzner Steven M Lewis Jared Adolf-Bryfogle Nawsad Alam Rebecca F Alford Melanie Aprahamian David Baker Kyle A Barlow Patrick Barth Benjamin Basanta Brian J Bender Kristin Blacklock Jaume Bonet Scott E Boyken Phil Bradley Chris Bystroff Patrick Conway Seth Cooper Bruno E Correia Brian Coventry Rhiju Das René M De Jong Frank DiMaio Lorna Dsilva Roland Dunbrack Alexander S Ford Brandon Frenz Darwin Y Fu Caleb Geniesse Lukasz Goldschmidt Ragul Gowthaman Jeffrey J Gray Dominik Gront Sharon Guffy Scott Horowitz Po-Ssu Huang Thomas Huber Tim M Jacobs Jeliazko R Jeliazkov David K Johnson Kalli Kappel John Karanicolas Hamed Khakzad Karen R Khar Sagar D Khare Firas Khatib Alisa Khramushin Indigo C King Robert Kleffner Brian Koepnick Tanja Kortemme Georg Kuenze Brian Kuhlman Daisuke Kuroda Jason W Labonte Jason K Lai Gideon Lapidoth Andrew Leaver-Fay Steffen Lindert Thomas Linsky Nir London Joseph H Lubin Sergey Lyskov Jack Maguire Lars Malmström Enrique Marcos Orly Marcu Nicholas A Marze Jens Meiler Rocco Moretti Vikram Khipple Mulligan Santrupti Nerli Christoffer Norn Shane Ó'Conchúir Noah Ollikainen Sergey Ovchinnikov Michael S Pacella Xingjie Pan Hahnbeom Park Ryan E Pavlovicz Manasi Pethe Brian G Pierce Kala Bharath Pilla Barak Raveh P Douglas Renfrew Shourya S Roy Burman Aliza Rubenstein Marion F Sauer Andreas Scheck William Schief Ora Schueler-Furman Yuval Sedan Alexander M Sevy Nikolaos G Sgourakis Lei Shi Justin B Siegel Daniel-Adriano Silva Shannon Smith Yifan Song Amelie Stein Maria Szegedy Frank D Teets Summer B Thyme Ray Yu-Ruei Wang Andrew Watkins Lior Zimmerman Richard Bonneau

Nat Methods 2020 07 1;17(7):665-680. Epub 2020 Jun 1.

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.

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July 2020

Allosteric conformational change of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy.

Proc Natl Acad Sci U S A 2020 05 1;117(20):10839-10847. Epub 2020 May 1.

Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195;

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May 2020

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Structure 2019 12 25;27(12):1745-1759. Epub 2019 Nov 25.

Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA. Electronic address:

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December 2019

Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis.

Nat Commun 2019 10 31;10(1):4959. Epub 2019 Oct 31.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.

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October 2019

The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach.

Structure 2019 09 11;27(9):1384-1394.e4. Epub 2019 Jul 11.

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY 10065, USA. Electronic address:

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September 2019

The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization.

Nat Struct Mol Biol 2019 08 8;26(8):686-694. Epub 2019 Jul 8.

Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.

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August 2019