De novo protein design by deep network hallucination

Anishchenko, Ivan; Pellock, Samuel J.; Chidyausiku, Tamuka M.; Ramelot, Theresa A.; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim K.; DiMaio, Frank; Carter, Lauren; Chow, Cameron M.; Montelione, Gaetano T.; Baker, David

doi:10.1038/s41586-021-04184-w

De novo protein design by deep network hallucination

Journal Article · 01 December 2021 · Nature

DOI:https://doi.org/10.1038/s41586-021-04184-w· OSTI ID:1844737

Anishchenko, Ivan; Pellock, Samuel J.; Chidyausiku, Tamuka M.; Ramelot, Theresa A.; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim K.; DiMaio, Frank; Carter, Lauren; Chow, Cameron M.; Montelione, Gaetano T.; Baker, David

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH); National Science Foundation (NSF)

OSTI ID:: 1844737

Journal Information:: Nature, Vol. 600

Country of Publication:: United States

Language:: ENGLISH

References (46)

Distance-based protein folding powered by deep learning Xu, Jinbo Proceedings of the National Academy of Sciences, Vol. 116, Issue 34 https://doi.org/10.1073/pnas.1821309116	journal	August 2019
Improved protein structure prediction using potentials from deep learning Senior, Andrew W.; Evans, Richard; Jumper, John Nature, Vol. 577, Issue 7792 https://doi.org/10.1038/s41586-019-1923-7	journal	January 2020
Improved protein structure prediction using predicted interresidue orientations Yang, Jianyi; Anishchenko, Ivan; Park, Hahnbeom Proceedings of the National Academy of Sciences, Vol. 117, Issue 3 https://doi.org/10.1073/pnas.1914677117	journal	January 2020
Low-N protein engineering with data-efficient deep learning Biswas, Surojit; Khimulya, Grigory; Alley, Ethan C. Nature Methods, Vol. 18, Issue 4 https://doi.org/10.1038/s41592-021-01100-y	journal	April 2021
Fast and Flexible Protein Design Using Deep Graph Neural Networks Strokach, Alexey; Becerra, David; Corbi-Verge, Carles Cell Systems, Vol. 11, Issue 4 https://doi.org/10.1016/j.cels.2020.08.016	journal	October 2020
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks Karimi, Mostafa; Zhu, Shaowen; Cao, Yue Journal of Chemical Information and Modeling, Vol. 60, Issue 12 https://doi.org/10.1021/acs.jcim.0c00593	journal	September 2020
Deep generative models for T cell receptor protein sequences Davidsen, Kristian; Olson, Branden J.; DeWitt, William S. eLife, Vol. 8 https://doi.org/10.7554/eLife.46935	journal	September 2019
IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation Eguchi, Raphael R.; Anand, Namrata; Choe, Christian A. PLOS Computational Biology https://doi.org/10.1101/2020.08.07.242347	posted_content	February 2022
Expanding functional protein sequence spaces using generative adversarial networks Repecka, Donatas; Jauniskis, Vykintas; Karpus, Laurynas Nature Machine Intelligence, Vol. 3, Issue 4 https://doi.org/10.1038/s42256-021-00310-5	journal	March 2021
Generating functional protein variants with variational autoencoders Hawkins-Hooker, Alex; Depardieu, Florence; Baur, Sebastien PLOS Computational Biology, Vol. 17, Issue 2 https://doi.org/10.1371/journal.pcbi.1008736	journal	February 2021
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13) Senior, Andrew W.; Evans, Richard; Jumper, John Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12 https://doi.org/10.1002/prot.25834	journal	August 2019
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Protein Structure Prediction Using Rosetta Rohl, Carol A.; Strauss, Charlie E. M.; Misura, Kira M. S. Methods in Enzymology https://doi.org/10.1016/S0076-6879(04)83004-0	book	January 2004
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules Park, Hahnbeom; Bradley, Philip; Greisen, Per Journal of Chemical Theory and Computation, Vol. 12, Issue 12 https://doi.org/10.1021/acs.jctc.6b00819	journal	November 2016
A microscale protein NMR sample screening pipeline Rossi, Paolo; Swapna, G. V. T.; Huang, Yuanpeng J. Journal of Biomolecular NMR, Vol. 46, Issue 1 https://doi.org/10.1007/s10858-009-9386-z	journal	November 2009
Principles for designing ideal protein structures Koga, Nobuyasu; Tatsumi-Koga, Rie; Liu, Gaohua Nature, Vol. 491, Issue 7423 https://doi.org/10.1038/nature11600	journal	November 2012
De novo design of a fluorescence-activating β-barrel Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William Nature, Vol. 561, Issue 7724 https://doi.org/10.1038/s41586-018-0509-0	journal	September 2018
Protein sequence design by conformational landscape optimization Norn, Christoffer; Wicky, Basile I. M.; Juergens, David Proceedings of the National Academy of Sciences, Vol. 118, Issue 11 https://doi.org/10.1073/pnas.2017228118	journal	March 2021
Accurate prediction of protein structures and interactions using a three-track neural network Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan Science, Vol. 373, Issue 6557 https://doi.org/10.1126/science.abj8754	journal	July 2021
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
TM-align: a protein structure alignment algorithm based on the TM-score Zhang, Y. Nucleic Acids Research, Vol. 33, Issue 7 https://doi.org/10.1093/nar/gki524	journal	April 2005
Protein production by auto-induction in high-density shaking cultures Studier, F. William Protein Expression and Purification, Vol. 41, Issue 1, p. 207-234 https://doi.org/10.1016/j.pep.2005.01.016	journal	May 2005
How to measure and predict the molar absorption coefficient of a protein Pace, C. Nick; Vajdos, Felix; Fee, Lanette Protein Science, Vol. 4, Issue 11 https://doi.org/10.1002/pro.5560041120	journal	November 1995
The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium Xiao, Rong; Anderson, Stephen; Aramini, James Journal of Structural Biology, Vol. 172, Issue 1 https://doi.org/10.1016/j.jsb.2010.07.011	journal	October 2010
High-level production of uniformly 15N-and 13C-enriched fusion proteins in Escherichia coli Jansson, Magnus; Li, Yu-Chin; Jendeberg, Lena Journal of Biomolecular NMR, Vol. 7, Issue 2 https://doi.org/10.1007/BF00203823	journal	March 1996
Measurement ofJand Dipolar Couplings from Simplified Two-Dimensional NMR Spectra Ottiger, Marcel; Delaglio, Frank; Bax, Ad Journal of Magnetic Resonance, Vol. 131, Issue 2 https://doi.org/10.1006/jmre.1998.1361	journal	April 1998
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy Lee, Woonghee; Tonelli, Marco; Markley, John L. Bioinformatics, Vol. 31, Issue 8 https://doi.org/10.1093/bioinformatics/btu830	journal	December 2014
NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers Favier, Adrien; Brutscher, Bernhard Journal of Biomolecular NMR, Vol. 73, Issue 5 https://doi.org/10.1007/s10858-019-00249-1	journal	May 2019
Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling Hyberts, Sven G.; Milbradt, Alexander G.; Wagner, Andreas B. Journal of Biomolecular NMR, Vol. 52, Issue 4 https://doi.org/10.1007/s10858-012-9611-z	journal	February 2012
Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data Ying, Jinfa; Delaglio, Frank; Torchia, Dennis A. Journal of Biomolecular NMR, Vol. 68, Issue 2 https://doi.org/10.1007/s10858-016-0072-7	journal	November 2016
I-PINE web server: an integrative probabilistic NMR assignment system for proteins Lee, Woonghee; Bahrami, Arash; Dashti, Hesam T. Journal of Biomolecular NMR, Vol. 73, Issue 5 https://doi.org/10.1007/s10858-019-00255-3	journal	May 2019
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks Shen, Yang; Bax, Ad Journal of Biomolecular NMR, Vol. 56, Issue 3 https://doi.org/10.1007/s10858-013-9741-y	journal	June 2013
Torsion angle dynamics for NMR structure calculation with the new program Dyana Güntert, P.; Mumenthaler, C.; Wüthrich, K. Journal of Molecular Biology, Vol. 273, Issue 1 https://doi.org/10.1006/jmbi.1997.1284	journal	October 1997
Protein NMR Recall, Precision, and F -measure Scores (RPF Scores): Structure Quality Assessment Measures Based on Information Retrieval Statistics Huang, Yuanpeng J.; Powers, Robert; Montelione, Gaetano T. Journal of the American Chemical Society, Vol. 127, Issue 6 https://doi.org/10.1021/ja047109h	journal	February 2005
A topology-constrained distance network algorithm for protein structure determination from NOESY data Huang, Yuanpeng Janet; Tejero, Roberto; Powers, Robert Proteins: Structure, Function, and Bioinformatics, Vol. 62, Issue 3 https://doi.org/10.1002/prot.20820	journal	December 2005
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination Brünger, A. T.; Adams, P. D.; Clore, G. M. Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5 https://doi.org/10.1107/S0907444998003254	journal	September 1998
Evaluating protein structures determined by structural genomics consortia Bhattacharya, Aneerban; Tejero, Roberto; Montelione, Gaetano T. Proteins: Structure, Function, and Bioinformatics, Vol. 66, Issue 4 https://doi.org/10.1002/prot.21165	journal	December 2006
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Improved low-resolution crystallographic refinement with Phenix and Rosetta DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J. Nature Methods, Vol. 10, Issue 11 https://doi.org/10.1038/nmeth.2648	journal	September 2013
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Accurate Structural Correlations from Maximum Likelihood Superpositions Theobald, Douglas L.; Wuttke, Deborah S. PLoS Computational Biology, Vol. 4, Issue 2 https://doi.org/10.1371/journal.pcbi.0040043	journal	January 2008
NMR: prediction of molecular alignment from structure using the PALES software Zweckstetter, Markus Nature Protocols, Vol. 3, Issue 4 https://doi.org/10.1038/nprot.2008.36	journal	March 2008
2D Chemical exchange NMR spectroscopy by proton-detected heteronuclear correlation Montelione, Gaetano T.; Wagner, Gerhard Journal of the American Chemical Society, Vol. 111, Issue 8 https://doi.org/10.1021/ja00190a072	journal	April 1989

Similar Records

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

Journal Article · 2016 · Science · OSTI ID:1355858

Boyken, S. E.; Chen, Z.; Groves, B.; +11 more

De novo design of functional proteins: Toward artificial hydrogenases: De Novo Design of Functional Proteins

Journal Article · 2013 · Biopolymers · OSTI ID:1383174

Faiella, Marina; Roy, Anindya; Sommer, Dayn; +1 more

De novo protein design by deep network hallucination

Citation Formats

References (46)

Similar Records

Related Subjects