Deep residual networks for crystallography trained on synthetic data

Mendez, Derek; Holton, James M.; Lyubimov, Artem Y.; Hollatz, Sabine; Mathews, Irimpan I.; Cichosz, Aleksander; Martirosyan, Vardan; Zeng, Teo; Stofer, Ryan; Liu, Ruobin; Song, Jinhu; McPhillips, Scott; Soltis, Mike; Cohen, Aina E.

doi:10.1107/S2059798323010586

Title: Deep residual networks for crystallography trained on synthetic data

Journal Article · 01 January 2024 · Acta Crystallographica. Section D. Structural Biology

DOI: https://doi.org/10.1107/S2059798323010586 · OSTI ID:2274863

Mendez, Derek; Holton, James M.; Lyubimov, Artem Y.; Hollatz, Sabine;

; Cichosz, Aleksander; Martirosyan, Vardan; Zeng, Teo; Stofer, Ryan;

; Song, Jinhu; McPhillips, Scott; Soltis, Mike;

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

View Journal Article

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 2274863

Journal Information:: Acta Crystallographica. Section D. Structural Biology, Journal Name: Acta Crystallographica. Section D. Structural Biology Journal Issue: 1 Vol. 80; ISSN ACSDAD; ISSN 2059-7983

Publisher:: International Union of Crystallography (IUCr)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

References (55)

Design of a hard X-ray beamline and end-station for pump and probe experiments at Pohang Accelerator Laboratory X-ray Free Electron Laser facility Park, Jaeku; Eom, Intae; Kang, Tai-Hee Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 810 https://doi.org/10.1016/j.nima.2015.11.147	journal	February 2016
Megapixels @ Megahertz – The AGIPD high-speed cameras for the European XFEL Allahgholi, Aschkan; Becker, Julian; Delfs, Annette Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 942 https://doi.org/10.1016/j.nima.2019.06.065	journal	October 2019
Serial synchrotron crystallography for time-resolved structural biology Pearson, Arwen R.; Mehrabi, Pedram Current Opinion in Structural Biology, Vol. 65 https://doi.org/10.1016/j.sbi.2020.06.019	journal	December 2020
Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature Fielding, Andrew J.; Dornevil, Kednerlin; Ma, Li Journal of the American Chemical Society, Vol. 139, Issue 48 https://doi.org/10.1021/jacs.7b08911	journal	November 2017
Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases Artz, Jacob H.; Zadvornyy, Oleg A.; Mulder, David W. Journal of the American Chemical Society, Vol. 142, Issue 3 https://doi.org/10.1021/jacs.9b08756	journal	December 2019
Determination of Absolute from Relative X-Ray Intensity Data Wilson, A. J. C. Nature, Vol. 150, Issue 3796 https://doi.org/10.1038/150152a0	journal	August 1942
Potential for biomolecular imaging with femtosecond X-ray pulses Neutze, Richard; Wouts, Remco; van der Spoel, David Nature, Vol. 406, Issue 6797 https://doi.org/10.1038/35021099	journal	August 2000
Femtosecond X-ray protein nanocrystallography Chapman, Henry N.; Fromme, Petra; Barty, Anton Nature, Vol. 470, Issue 7332, p. 73-77 https://doi.org/10.1038/nature09750	journal	February 2011
Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature Sellberg, J. A.; Huang, C.; McQueen, T. A. Nature, Vol. 510, Issue 7505 https://doi.org/10.1038/nature13266	journal	June 2014
The Coherent X-ray Imaging Data Bank Maia, Filipe R. N. C. Nature Methods, Vol. 9, Issue 9 https://doi.org/10.1038/nmeth.2110	journal	August 2012
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
Megahertz serial crystallography Wiedorn, Max O.; Oberthür, Dominik; Bean, Richard Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06156-7	journal	October 2018
A unifying Bayesian framework for merging X-ray diffraction data Dalton, Kevin M.; Greisman, Jack B.; Hekstra, Doeke R. Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-35280-8	journal	December 2022
Ultrafast structural changes direct the first molecular events of vision Gruhl, Thomas; Weinert, Tobias; Rodrigues, Matthew J. Nature, Vol. 615, Issue 7954 https://doi.org/10.1038/s41586-023-05863-6	journal	March 2023
Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector Leonarski, Filip; Redford, Sophie; Mozzanica, Aldo Nature Methods, Vol. 15, Issue 10 https://doi.org/10.1038/s41592-018-0143-7	journal	October 2018
Time-resolved serial femtosecond crystallography at the European XFEL Pandey, Suraj; Bean, Richard; Sato, Tokushi Nature Methods https://doi.org/10.1038/s41592-019-0628-z	journal	November 2019
A new era of synchrotron-enabled macromolecular crystallography Cohen, Aina E. Nature Methods, Vol. 18, Issue 5 https://doi.org/10.1038/s41592-021-01146-y	journal	May 2021
Goniometer-based femtosecond crystallography with X-ray free electron lasers Cohen, Aina E.; Soltis, S. Michael; González, Ana Proceedings of the National Academy of Sciences, Vol. 111, Issue 48, p. 17122-17127 https://doi.org/10.1073/pnas.1418733111	journal	October 2014
Time-Resolved Crystallography at X-ray Free Electron Lasers and Synchrotron Light Sources Schmidt, Marius Synchrotron Radiation News, Vol. 28, Issue 6 https://doi.org/10.1080/08940886.2015.1101324	journal	November 2015
XCVII. The intensity of reflexion of X rays by crystals Bragg, W. H. The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, Vol. 27, Issue 161 https://doi.org/10.1080/14786440508635159	journal	May 1914
Superconducting cavity material for the European XFEL Singer, W.; Singer, X.; Brinkmann, A. Superconductor Science and Technology, Vol. 28, Issue 8 https://doi.org/10.1088/0953-2048/28/8/085014	journal	July 2015
Watching proteins function with time-resolved x-ray crystallography Šrajer, Vukica; Schmidt, Marius Journal of Physics D: Applied Physics, Vol. 50, Issue 37 https://doi.org/10.1088/1361-6463/aa7d32	journal	August 2017
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
FabIO: easy access to two-dimensional X-ray detector images in Python Knudsen, Erik B.; Sørensen, Henning O.; Wright, Jonathan P. Journal of Applied Crystallography, Vol. 46, Issue 2 https://doi.org/10.1107/S0021889813000150	journal	February 2013
Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures Kmetko, Jan; Husseini, Naji S.; Naides, Matthew Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9 https://doi.org/10.1107/S0907444906023869	journal	August 2006
The minimum crystal size needed for a complete diffraction data set Holton, James M.; Frankel, Kenneth A. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007262	journal	March 2010
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
AutoDrug : fully automated macromolecular crystallography workflows for fragment-based drug discovery Tsai, Yingssu; McPhillips, Scott E.; González, Ana Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 5 https://doi.org/10.1107/S0907444913001984	journal	April 2013
Blu-Ice and the Distributed Control System : software for data acquisition and instrument control at macromolecular crystallography beamlines McPhillips, Timothy M.; McPhillips, Scott E.; Chiu, Hsiu-Ju Journal of Synchrotron Radiation, Vol. 9, Issue 6 https://doi.org/10.1107/S0909049502015170	journal	November 2002
A beginner's guide to radiation damage Holton, James M. Journal of Synchrotron Radiation, Vol. 16, Issue 2 https://doi.org/10.1107/S0909049509004361	journal	February 2009
New methods for indexing multi-lattice diffraction data Gildea, Richard J.; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10 https://doi.org/10.1107/S1399004714017039	journal	September 2014
GrainSpotter : a fast and robust polycrystalline indexing algorithm Schmidt, Søren Journal of Applied Crystallography, Vol. 47, Issue 1 https://doi.org/10.1107/S1600576713030185	journal	January 2014
Recent developments in CrystFEL White, Thomas A.; Mariani, Valerio; Brehm, Wolfgang Journal of Applied Crystallography, Vol. 49, Issue 2 https://doi.org/10.1107/S1600576716004751	journal	March 2016
OnDA : online data analysis and feedback for serial X-ray imaging Mariani, Valerio; Morgan, Andrew; Yoon, Chun Hong Journal of Applied Crystallography, Vol. 49, Issue 3 https://doi.org/10.1107/S1600576716007469	journal	May 2016
Stable sample delivery in a viscous medium via a polyimide-based single-channel microfluidic chip for serial crystallography Nam, Ki Hyun; Cho, Yunje Journal of Applied Crystallography, Vol. 54, Issue 4 https://doi.org/10.1107/S1600576721005720	journal	July 2021
Data reduction for X-ray serial crystallography using machine learning Rahmani, Vahid; Nawaz, Shah; Pennicard, David Journal of Applied Crystallography, Vol. 56, Issue 1 https://doi.org/10.1107/S1600576722011748	journal	February 2023
The X-ray Pump–Probe instrument at the Linac Coherent Light Source Chollet, Matthieu; Alonso-Mori, Roberto; Cammarata, Marco Journal of Synchrotron Radiation, Vol. 22, Issue 3 https://doi.org/10.1107/S1600577515005135	journal	April 2015
A convolutional neural network-based screening tool for X-ray serial crystallography Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X. Journal of Synchrotron Radiation, Vol. 25, Issue 3, p. 655-670 https://doi.org/10.1107/S1600577518004873	journal	April 2018
On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies Lieske, Julia; Cerv, Maximilian; Kreida, Stefan IUCrJ, Vol. 6, Issue 4 https://doi.org/10.1107/S2052252519007395	journal	June 2019
High-density grids for efficient data collection from multiple crystals Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1, p. 2-11 https://doi.org/10.1107/S2059798315020847	journal	January 2016
EIGER detector: application in macromolecular crystallography Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D. Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9 https://doi.org/10.1107/S2059798316012304	journal	August 2016
DIALS : implementation and evaluation of a new integration package Winter, Graeme; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317017235	journal	February 2018
Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction Sauter, Nicholas K.; Kern, Jan; Yano, Junko Acta Crystallographica Section D Structural Biology, Vol. 76, Issue 2 https://doi.org/10.1107/S2059798320000418	journal	February 2020
Best practices for time-resolved serial synchrotron crystallography Schulz, Eike C.; Yorke, Briony A.; Pearson, Arwen R. Acta Crystallographica Section D Structural Biology, Vol. 78, Issue 1 https://doi.org/10.1107/S2059798321011621	journal	January 2022
Gradient-based learning applied to document recognition Lecun, Y.; Bottou, L.; Bengio, Y. Proceedings of the IEEE, Vol. 86, Issue 11 https://doi.org/10.1109/5.726791	journal	January 1998
The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures Holton, James M.; Classen, Scott; Frankel, Kenneth A. The FEBS Journal, Vol. 281, Issue 18 https://doi.org/10.1111/febs.12922	journal	September 2014
The CSPAD megapixel x-ray camera at LCLS Hart, Philip; Boutet, Sébastien; Carini, Gabriella SPIE Optical Engineering + Applications, SPIE Proceedings https://doi.org/10.1117/12.930924	conference	October 2012
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography Boutet, S.; Lomb, L.; Williams, G. J. Science, Vol. 337, Issue 6092 https://doi.org/10.1126/science.1217737	journal	May 2012
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
Advances and challenges in time-resolved macromolecular crystallography Brändén, Gisela; Neutze, Richard Science, Vol. 373, Issue 6558 https://doi.org/10.1126/science.aba0954	journal	August 2021
Potential of Time-Resolved Serial Femtosecond Crystallography Using High Repetition Rate XFEL Sources de Wijn, Raphaël; Melo, Diogo V. M.; Koua, Faisal H. M. Applied Sciences, Vol. 12, Issue 5 https://doi.org/10.3390/app12052551	journal	February 2022
SwissFEL: The Swiss X-ray Free Electron Laser Milne, Christopher; Schietinger, Thomas; Aiba, Masamitsu Applied Sciences, Vol. 7, Issue 7 https://doi.org/10.3390/app7070720	journal	July 2017
Pump-Probe Time-Resolved Serial Femtosecond Crystallography at SACLA: Current Status and Data Collection Strategies Nango, Eriko; Kubo, Minoru; Tono, Kensuke Applied Sciences, Vol. 9, Issue 24 https://doi.org/10.3390/app9245505	journal	December 2019
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Zeldin, Oliver B. eLife, Vol. 5 https://doi.org/10.7554/eLife.18740	journal	October 2016

Similar Records

A convolutional neural network-based screening tool for X-ray serial crystallography

Journal Article · 2018 · Journal of Synchrotron Radiation (Online) · OSTI ID:1434392

Ke, Tsung-Wei; Brewster, Aaron S.; Yu, Stella X.; +3 more

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

Journal Article · 2009 · Acta Crystallogr.D Biol.Crystallogr.D64:1210,2008 · OSTI ID:953572

Soltis, S M; Cohen, A E; Deacon, A; +18 more

The Stanford Automated Mounter: Pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines

Journal Article · 2016 · Journal of Applied Crystallography (Online) · OSTI ID:1253923

Russi, Silvia; Song, Jinhu; McPhillips, Scott E.; +1 more

Related Subjects

36 MATERIALS SCIENCE
XFELs
artificial intelligence
rotation crystallography
serial crystallography
synchrotrons

Title: Deep residual networks for crystallography trained on synthetic data

Citation Formats

References (55)

Similar Records

Related Subjects