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Author Details

James M Holton
Lawrence Berkeley National Laboratory
1997
72
44
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36702895Large language models generate functional protein sequences across diverse families.Nat Biotechnol2023
37723259Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.Nat Chem2023
37138085Structural evidence for intermediates during O<sub>2</sub> formation in photosystem II.Nature2023
37369071Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography.J Am Chem Soc2023
35169801The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature.bioRxiv2022
35622909The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.Sci Adv2022
34117122Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map.Proc Natl Acad Sci U S A2021
33853786Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.Sci Adv2021
33814275Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase).J Biosci Bioeng2021
34764256Structural dynamics in the water and proton channels of photosystem II during the S<sub>2</sub> to S<sub>3</sub> transition.Nat Commun2021
32434915Untangling the sequence of events during the S<sub>2</sub> â¿¿ S<sub>3</sub> transition in photosystem II and implications for the water oxidation mechanism.Proc Natl Acad Sci U S A2020
32047034Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.Proc Natl Acad Sci U S A2020
32038048Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction.Acta Crystallogr D Struct Biol2020
33209326Beyond integration: modeling every pixel to obtain better structure factors from stills.IUCrJ2020
30821701Challenge data set for macromolecular multi-microcrystallography.Acta Crystallogr D Struct Biol2019
30853418Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite.Cell Chem Biol2019
30405241Structures of the intermediates of Kok's photosynthetic water oxidation clock.Nature2018
28892041Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.Nat Struct Mol Biol2017
28440794Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin.Sci Data2017
28375150Responses to `Atomic resolution': a badly abused term in structural biology.Acta Crystallogr D Struct Biol2017
27811937Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.Nat Commun2016
27731796Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.Elife2016
25532136Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.Nat Methods2015
26422513Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.Elife2015
25865481Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion.Cell2015
24363322Protein structural ensembles are revealed by redefining X-ray electron density noise.Proc Natl Acad Sci U S A2014
25362050Goniometer-based femtosecond crystallography with X-ray free electron lasers.Proc Natl Acad Sci U S A2014
25040949The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures.FEBS J2014
24843173Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC.Proc Natl Acad Sci U S A2014
23396808Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.J Appl Crystallogr2013
24297937Predicting the X-ray lifetime of protein crystals.Proc Natl Acad Sci U S A2013
23631449Peptide crystal simulations reveal hidden dynamics.J Am Chem Soc2013
23793149Crystallographic data processing for free-electron laser sources.Acta Crystallogr D Biol Crystallogr2013
22330507Time-resolved protein nanocrystallography using an X-ray free-electron laser.Opt Express2012
23093762The point-spread function of fiber-coupled area detectors.J Synchrotron Radiat2012
21369108Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals.Opt Express2011
24089594Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.Phys Rev B Condens Matter Mater Phys2011
21788488Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces.Proc Natl Acad Sci U S A2011
21918110Accessing protein conformational ensembles using room-temperature X-ray crystallography.Proc Natl Acad Sci U S A2011
21325716Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals.Acta Crystallogr A2011
21293373Femtosecond X-ray protein nanocrystallography.Nature2011
20382993The minimum crystal size needed for a complete diffraction data set.Acta Crystallogr D Biol Crystallogr2010
20975223Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system.J Synchrotron Radiat2010
20499387Automated electron-density sampling reveals widespread conformational polymorphism in proteins.Protein Sci2010
20389587Femtosecond protein nanocrystallography-data analysis methods.Opt Express2010
19240325A beginner's guide to radiation damage.J Synchrotron Radiat2009
20463854An assessment of the resolution limitation due to radiation-damage in x-ray diffraction microscopy.J Electron Spectros Relat Phenomena2009
191487742007 annual progress report synopsis of the Center for Structures of Membrane Proteins.J Struct Funct Genomics2009
19240326Determination of X-ray flux using silicon pin diodes.J Synchrotron Radiat2009
19172748Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75.Nat Struct Mol Biol2008
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Collaborators

Tom Alber
University of California berkeley
Co-authored papers 12
James S Fraser
University of California san francisco
Co-authored papers 9
Paul D Adams
Lawrence Berkeley National Laboratory
Co-authored papers 6
Iris D Young
University of California san francisco
Co-authored papers 5
Petra Fromme
Biodesign Center for Applied Structural Discovery, Arizona State University
Co-authored papers 5
Michael C Thompson
University of California
Co-authored papers 5
Galen J Correy
University of California san francisco
Co-authored papers 3
Thomas C Terwilliger
Los Alamos National Laboratory
Co-authored papers 3
John A Tainer
The University of Texas MD Anderson Cancer Center
Co-authored papers 3
Daniel L Minor
Cardiovascular Research Institute, University of California san francisco
Co-authored papers 3
Henry van den Bedem
University of California San Francisco
Co-authored papers 2
Randy J Read
Cambridge Institute for Medical Research, University of Cambridge
Co-authored papers 2
Greg L Hura
Lawrence Berkeley National Laboratory, University of California Santa Cruz
Co-authored papers 2
Michal Hammel
Lawrence Berkeley National Laboratory
Co-authored papers 2
Robert M Stroud
University of California San Francisco
Co-authored papers 2
Alan Ashworth
UCSF Helen Diller Family Comprehensive Cancer Center
Co-authored papers 2
Wesley I Sundquist
University of Utah School of Medicine
Co-authored papers 2
Aashish Manglik
Department of Pharmaceutical Chemistry, University of California San Francisco
Co-authored papers 1
David A Agard
University of California, USA Quantitative Biosciences Institute (QBI) san francisco
Co-authored papers 1
Martine F Roussel
St. Jude Children's Research Hospital
Co-authored papers 1
Nadia Herrera
University of California san francisco
Co-authored papers 1
Ishan Deshpande
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 1
Janet Finer-Moore
University of California San Francisco
Co-authored papers 1
Su Guo
University of California san francisco
Co-authored papers 1
Robert J Fletterick
University of California San Francisco
Co-authored papers 1
Pamela J Bjorkman
Co-authored papers 1
John J Irwin
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 1
Brian K Shoichet
Department of Pharmaceutical Chemistry, University of California san francisco
Co-authored papers 1
Avi J Samelson
Institute for Neurodegenerative Diseases, University of California san francisco
Co-authored papers 1
Huong T Kratochvil
Department of Pharmaceutical Chemistry, University of California-San Francisco
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