P. Zwart

发表

K-means-driven Gaussian Process data collection for angle-resolved photoemission spectroscopy

C. Melton, M. Noack, T. Ohta, 2020, Mach. Learn. Sci. Technol..

De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity

Robert A. Langan, J. H. Pereira, D. Baker, 2016, Science.

Computational Design of Self-Assembling Cyclic Protein Homo-oligomers

J. H. Pereira, D. Baker, P. Zwart, 2016, Nature chemistry.

Structural Determinants Underlying Photoprotection in the Photoactive Orange Carotenoid Protein of Cyanobacteria

P. Zwart, M. Klein, C. Kerfeld, 2010, The Journal of Biological Chemistry.

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, 2010, Journal of applied crystallography.

Crystal Structure of an Archaeal Class I Aldolase and the Evolution of (βα)8 Barrel Proteins*

P. Zwart, R. Russell, A. Stark, 2003, Journal of Biological Chemistry.

Towards automated crystallographic structure refinement with phenix.refine

P. Zwart, P. Adams, T. Terwilliger, 2012, Acta crystallographica. Section D, Biological crystallography.

Principles for designing proteins with cavities formed by curved β sheets

Gaohua Liu, Gaetano T. Montelione, Yuefeng Tang, 2017, Science.

Electronic Reprint Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard Biological Crystallography Decision-making in Structure Solution Using Bayesian Estimates of Map Quality: the Phenix Autosol Wizard

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2022 .

Shapes and vorticities of superfluid helium nanodroplets

Stephen R. Leone, Alexander Hexemer, Jonathan H. Ma, 2014, Science.

Surprises and pitfalls arising from (pseudo)symmetry

P. Zwart, P. Adams, G. Murshudov, 2007, Acta crystallographica. Section D, Biological crystallography.

Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus.

P. Zwart, R. Read, E. Dodson, 2012, Acta crystallographica. Section D, Biological crystallography.

Detection and correction of underassigned rotational symmetry prior to structure deposition

Nicholas K. Sauter, Ralf W. Grosse-Kunstleve, Peter H. Zwart, 2010, Acta crystallographica. Section D, Biological crystallography.

Breaking good resolutions with ARP/wARP.

Victor S Lamzin, Serge X. Cohen, Anastassis Perrakis, 2004, Journal of synchrotron radiation.

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing

Paul D. Adams, Thomas C. Terwilliger, Peter H. Zwart, 2016, Acta crystallographica. Section D, Structural biology.

Anomalous signal indicators in protein crystallography.

P. Zwart, P H Zwart, 2005, Acta crystallographica. Section D, Biological crystallography.

Determining pair distance distribution function from SAXS data using parametric functionals.

Haiguang Liu, Peter H Zwart, P. Zwart, 2012, Journal of structural biology.

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal

Thomas C Terwilliger, Paul D Adams, Peter H Zwart, 2016, Acta crystallographica. Section D, Structural biology.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

Sébastien Boutet, Nathaniel Echols, Marc Messerschmidt, 2014, Nature Methods.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals

Sébastien Boutet, Nathaniel Echols, Marc Messerschmidt, 2012, Proceedings of the National Academy of Sciences.

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

D. Baker, P. Zwart, M. J. Bick, 2020, eLife.

No observable conformational changes in PSII

P. Zwart, P. Adams, N. Echols, 2016, Nature.

Structural basis for substrate specificity differences of horse liver alcohol dehydrogenase isozymes.

V Lamzin, P. Zwart, V. Lamzin, 2000, Biochemistry.

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase.

G. Whitesides, P. Zwart, W. Sherman, 2017, Angewandte Chemie.

Structures of cGMP-Dependent Protein Kinase (PKG) Iα Leucine Zippers Reveal an Interchain Disulfide Bond Important for Dimer Stability.

P. Zwart, Choel Kim, D. Casteel, 2015, Biochemistry.

Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity

P. Zwart, R. Brennan, P. Kiley, 2013, Nature Structural &Molecular Biology.

Three-dimensional single-particle imaging using angular correlations from X-ray laser data.

P. Zwart, J. Spence, D. Saldin, 2013, Acta crystallographica. Section A, Foundations of crystallography.

New Science Opportunities Enabled by LCLS-II X-ray Lasers

Anton Barty, Sebastian Doniach, Paul D. Adams, 2015 .

Deep learning-based identification of sub-nuclear structures in FIB-SEM images

P. Zwart, H. Hess, C. Xu, 2022, 2207.09598.

Improved crystal orientation and physical properties from single-shot XFEL stills

P. Zwart, P. Adams, N. Echols, 2014, Acta crystallographica. Section D, Biological crystallography.

Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials.

P. Zwart, A. Janssen, Haiguang Liu, 2012, Acta crystallographica. Section A, Foundations of crystallography.

Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases.

P. Zwart, B. Sankaran, Laura Riccardi, 2018, Biochemistry.

Structure determination of LpxD from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

P. Zwart, B. Sankaran, V. Nienaber, 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.

Structure of photosystem II and substrate binding at room temperature

Marcin Sikorski, Nicholas K. Sauter, Paul D. Adams, 2016, Nature.

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.

P. Zwart, S. Ealick, Yang Zhang, 2012, Acta crystallographica. Section D, Biological crystallography.

Simultaneous detection of electronic structure changes from two elements of a bifunctional catalyst using wavelength-dispersive X-ray emission spectroscopy and in situ electrochemistry.

P. Zwart, D. Sokaras, T. Jaramillo, 2015, Physical chemistry chemical physics : PCCP.

The influence of positional errors on the Debye effects.

P. Zwart, V. Lamzin, 2004, Acta crystallographica. Section D, Biological crystallography.

The structure of LpxD from Pseudomonas aeruginosa at 1.3 Å resolution.

P. Zwart, B. Sankaran, V. Nienaber, 2011, Acta crystallographica. Section F, Structural biology and crystallization communications.

Accelerated Macromolecular Solution Structure Recovery

P. Zwart, Haiguang Liu, 2011 .

Free-electron laser data for multiple-particle fluctuation scattering analysis

P. Zwart, M. Bogan, M. Seibert, 2018, Scientific Data.

Acta Crystallographica Section D Biological

Randy J. Read, Airlie J. McCoy, Paul D. Adams, 2003 .

Iterative phasing for fluctuation X-ray scattering

Peter H Zwart, James A Sethian, J. Sethian, 2015, Proceedings of the National Academy of Sciences.

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature

Sébastien Boutet, Nathaniel Echols, Marc Messerschmidt, 2013, Science.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode

Sébastien Boutet, Nathaniel Echols, Nicholas K Sauter, 2012, Proceedings of the National Academy of Sciences.

Nanoflow electrospinning serial femtosecond crystallography.

Sébastien Boutet, Nathaniel Echols, Nicholas K Sauter, 2012, Acta crystallographica. Section D, Biological crystallography.

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Randy J. Read, Paul D. Adams, Gerard J. Kleywegt, 2011, Structure.

The Berkeley Center for Structural Biology at the Advanced Light Source

P. Zwart, G. Fontenay, P. Adams, 2015 .

Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2007 .

The Phenix software for automated determination of macromolecular structures.

Nathaniel Echols, Randy J Read, Gábor Bunkóczi, 2011, Methods.

Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

Aaron Stein, James A. Sethian, Guillaume Freychet, 2021, Nature Reviews Physics.

Resonant Soft X-Ray Scattering Provides Protein Structure with Chemical Specificity.

P. Zwart, Chenhui Zhu, T. Le, 2018, Structure.

Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport Citation

P. Zwart, S. Chisholm, M. Klein, 2011 .

Automated structure solution with the PHENIX suite.

Randy J Read, Nicholas K Sauter, Thomas C Terwilliger, 2008, Methods in molecular biology.

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

D. Baker, P. Zwart, M. J. Bick, 2020, bioRxiv.

A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.

Emily C. Hartman, P. Zwart, B. Sankaran, 2016, Nano letters.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2007, Acta crystallographica. Section D, Biological crystallography.

Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-ray Diffraction and Spectroscopy

Nicholas K. Sauter, Paul D. Adams, Sébastien Boutet, 2014, Nature Communications.

Gaussian Processes for Autonomous Data Acquisition at Large-Scale Synchrotron and Neutron Scattering Facilities

Katherine C. Elbert, Sethian, Christopher B. Murray, 2021 .

Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine β-Lactamases by Relieving Steric Strain.

P. Zwart, B. Sankaran, B. Prasad, 2016, Biochemistry.

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

David Baker, William Sheffler, Peter H Zwart, 2016, Proceedings of the National Academy of Sciences.

Chromohalobacter salixigens Uronate Dehydrogenase: Directed Evolution for Improved Thermal Stability and Mutant CsUDH-inc X-ray Crystal Structure.

J. H. Pereira, P. Zwart, B. Sankaran, 2020, Process biochemistry.

Autoindexing the diffraction patterns from crystals with a pseudotranslation

Nicholas K. Sauter, Peter H. Zwart, P. Zwart, 2009, Acta crystallographica. Section D, Biological crystallography.

Analysis of the Binding Forces Driving the Tight Interactions between β-Lactamase Inhibitory Protein-II (BLIP-II) and Class A β-Lactamases*

P. Zwart, B. Sankaran, B. Prasad, 2011, The Journal of Biological Chemistry.

Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering.

S. Marchesini, P. Zwart, A. Hexemer, 2012, Journal of synchrotron radiation.

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

Randy J. Read, Paul D. Adams, Ralf W. Grosse-Kunstleve, 2008, Acta crystallographica. Section D, Biological crystallography.

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials.

Scott Grandison, Alexander Hexemer, Haiguang Liu, 2012, Acta crystallographica. Section A, Foundations of crystallography.

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Nicholas K. Sauter, Grant J. Jensen, Ariana Peck, 2020, bioRxiv.

Model Building

P. Zwart, T. Terwilliger, P. Afonine, 2003 .

Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport.

Cheryl A Kerfeld, Sabine Heinhorst, Peter Zwart, 2009, Journal of molecular biology.

The Small Angle Scattering ToolBox (SASTBX): an open-source software for biomolecular small-angle scattering

Alexander Hexemer, Haiguang Liu, Peter H. Zwart, 2012 .

Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

P. Zwart, B. Sankaran, V. Nienaber, 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.

The crystal structures of PKG Iβ (92-227) with cGMP and cAMP reveal the molecular details of cyclic-nucleotide binding

P. Zwart, T. Palzkill, J. Headd, 2011, BMC Pharmacology.

Co-Crystal Structures of PKG Iβ (92–227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding

Timothy Palzkill, Gilbert Huang, Jeffrey J Headd, 2011, PloS one.

Evaluating crystallographic likelihood functions using numerical quadratures

Petrus H. Zwart, Elliott D. Perryman, P. Zwart, 2020, bioRxiv.

Minimally disruptive optical control of protein tyrosine phosphatase 1B

P. Zwart, B. Sankaran, A. Hongdusit, 2019, Nature Communications.

Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation.

P. Zwart, B. Sankaran, M. Sousa, 2018, Biochemistry.

Automated structure determination with phenix

Randy J. Read, Airlie J. McCoy, Laurent C. Storoni, 2006 .

EWALD: A macromolecular diffractometer for the second target station.

Jiao Y. Y. Lin, P. Zwart, G. Borgstahl, 2022, Review of Scientific Instruments.

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

Peter H Zwart, James A Sethian, J. Sethian, 2017, Proceedings of the National Academy of Sciences.

Xi-cam: a versatile interface for data visualization and analysis.

Singanallur Venkatakrishnan, Zhang Jiang, Talita Perciano, 2018, Journal of synchrotron radiation.

SAD phasing of XFEL data depends critically on the error model

Nicholas K Sauter, Asmit Bhowmick, Aaron S Brewster, 2019, Acta crystallographica. Section D, Structural biology.

Modelling bound ligands in protein crystal structures.

V S Lamzin, P. Zwart, V. Lamzin, 2004, Acta crystallographica. Section D, Biological crystallography.

Computational Strategies to Increase Efficiency of Gaussian-Process-Driven Autonomous Experiments

Petrus Zwart, Marcus Noack, M. Noack, 2019, 2019 IEEE/ACM 1st Annual Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP).

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses.

Carl Nettelblad, Petra Fromme, Garth J. Williams, 2017, Physical review letters.

GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering

P. Zwart, Christine M. Sweeney, J. Donatelli, 2021, Journal of applied crystallography.

Ab initio structure determination from experimental fluctuation X-ray scattering data

Christoph Bostedt, Lutz Foucar, Ilme Schlichting, 2018, Proceedings of the National Academy of Sciences.

Operational properties of fluctuation X-ray scattering data

P. Zwart, C. Kerfeld, Erik Malmerberg, 2015, IUCrJ.

Coherent diffractive imaging of microtubules using an X-ray laser

Anton Barty, Sébastien Boutet, Henry N. Chapman, 2019, Nature Communications.

Biological Crystallography Structural Effects of Radiation Damage and Its Potential for Phasing

Zbigniew Dauter, P. Zwart, S. Banumathi, 2022 .

Acta Crystallographica Section D Biological

Vincent B. Chen, Ian W. Davis, Gary J. Kapral, 2001 .

Characterization of X-ray data sets

Paul D. Adams, Peter H. Zwart, Ralf W. Grosse-Kunsteleve, 2005 .

Distance distributions and electron-density characteristics of protein models.

P. Zwart, V. Lamzin, 2003, Acta crystallographica. Section D, Biological crystallography.

optical control 1B.

P. Zwart, B. Sankaran, A. Hongdusit, 2020 .

Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

P. Zwart, W. Baumeister, B. Jap, 2010, Nature Structural &Molecular Biology.

Observation of the 60Fe nucleosynthesis-clock isotope in galactic cosmic rays

Robert A. Langan, P. Zwart, Alex Ford, 2016, Science.

Automated structure solution with the PHENIX suite.

P. Zwart, R. Read, P. Adams, 2008, Methods in molecular biology.

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature

P. Zwart, M. Bogan, S. Boutet, 2013, Science.

Structure determination of LpxA from the lipopolysaccharide-synthesis pathway of Acinetobacter baumannii.

P. Zwart, B. Sankaran, V. Nienaber, 2012, Acta crystallographica. Section F, Structural biology and crystallization communications.

Towards automated crystallographic structure refinement with phenix.refine

P. Zwart, P. Adams, T. Terwilliger, 2012, Acta crystallographica. Section D, Biological crystallography.

Electronic Reprint Biological Crystallography Iterative Model Building, Structure Refinement and Density Modification with the Phenix Autobuild Wizard Biological Crystallography Iterative Model Building, Structure Refinement and Density Modification with the Phenix Autobuild Wizard

P. Zwart, R. Read, P. Adams, 2022 .

Computation of fluctuation scattering profiles via three-dimensional Zernike polynomials.

P. Zwart, A. Janssen, Haiguang Liu, 2012, Acta crystallographica. Section A, Foundations of crystallography.

Thermolysin structure determined by free-electron laser

P. Zwart, M. Bogan, S. Boutet, 2014 .

Structural Determinants Underlying Photoprotection in the Photoactive Orange Carotenoid Protein of Cyanobacteria

P. Zwart, M. Klein, C. Kerfeld, 2010, Journal of Biological Chemistry.