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De novo design of protein structure and function with RFdiffusion

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Cited by:

  1. Wei Lu & Jixian Zhang & Weifeng Huang & Ziqiao Zhang & Xiangyu Jia & Zhenyu Wang & Leilei Shi & Chengtao Li & Peter G. Wolynes & Shuangjia Zheng, 2024. "DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  2. Patrick Bryant & Atharva Kelkar & Andrea Guljas & Cecilia Clementi & Frank Noé, 2024. "Structure prediction of protein-ligand complexes from sequence information with Umol," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  3. Isak S. Pretorius & Thomas A. Dixon & Michael Boers & Ian T. Paulsen & Daniel L. Johnson, 2025. "The coming wave of confluent biosynthetic, bioinformational and bioengineering technologies," Nature Communications, Nature, vol. 16(1), pages 1-8, December.
  4. Timothy Atkinson & Thomas D. Barrett & Scott Cameron & Bora Guloglu & Matthew Greenig & Charlie B. Tan & Louis Robinson & Alex Graves & Liviu Copoiu & Alexandre Laterre, 2025. "Protein sequence modelling with Bayesian flow networks," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  5. Shunshi Kohyama & Béla P. Frohn & Leon Babl & Petra Schwille, 2024. "Machine learning-aided design and screening of an emergent protein function in synthetic cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  6. Simon d’Oelsnitz & Daniel J. Diaz & Wantae Kim & Daniel J. Acosta & Tyler L. Dangerfield & Mason W. Schechter & Matthew B. Minus & James R. Howard & Hannah Do & James M. Loy & Hal S. Alper & Y. Jessie, 2024. "Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  7. Daniel R. Fox & Kazem Asadollahi & Imogen Samuels & Bradley A. Spicer & Ashleigh Kropp & Christopher J. Lupton & Kevin Lim & Chunxiao Wang & Hari Venugopal & Marija Dramicanin & Gavin J. Knott & Rhys , 2025. "Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  8. Ryan D. Kibler & Sangmin Lee & Madison A. Kennedy & Basile I. M. Wicky & Stella M. Lai & Marius M. Kostelic & Ann Carr & Xinting Li & Cameron M. Chow & Tina K. Nguyen & Lauren Carter & Vicki H. Wysock, 2024. "Design of pseudosymmetric protein hetero-oligomers," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  9. Xiaorui Wang & Xiaodan Yin & Dejun Jiang & Huifeng Zhao & Zhenxing Wu & Odin Zhang & Jike Wang & Yuquan Li & Yafeng Deng & Huanxiang Liu & Pei Luo & Yuqiang Han & Tingjun Hou & Xiaojun Yao & Chang-Yu , 2024. "Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  10. Gary Marchionini, 2024. "Information and library professionals' roles and responsibilities in an AI‐augmented world," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 75(8), pages 865-868, August.
  11. Wei Yang & Derrick R. Hicks & Agnidipta Ghosh & Tristin A. Schwartze & Brian Conventry & Inna Goreshnik & Aza Allen & Samer F. Halabiya & Chan Johng Kim & Cynthia S. Hinck & David S. Lee & Asim K. Ber, 2025. "Design of high-affinity binders to immune modulating receptors for cancer immunotherapy," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  12. Haseong Kim & Nathan J. Hillson & Byung-Kwan Cho & Bong Hyun Sung & Dae-Hee Lee & Dong-Myung Kim & Min-Kyu Oh & Matthew Wook Chang & Yong-Su Jin & Susan J. Rosser & Peter Vegh & Rennos Fragkoudis & Ro, 2025. "Abstraction hierarchy to define biofoundry workflows and operations for interoperable synthetic biology research and applications," Nature Communications, Nature, vol. 16(1), pages 1-6, December.
  13. Arne Matthys & Jan Felix & Joao Paulo Portela Catani & Kenny Roose & Wim Nerinckx & Benthe Buyten & Daria Fijalkowska & Nico Callewaert & Savvas N. Savvides & Xavier Saelens, 2025. "Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
  14. Xin Zhang & Zakir Ibrahim & Muhammad Bilawal Khaskheli & Hamad Raza & Fanrui Zhou & Imran Haider Shamsi, 2024. "Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications," Sustainability, MDPI, vol. 16(17), pages 1-26, September.
  15. Lucien F. Krapp & Fernando A. Meireles & Luciano A. Abriata & Jean Devillard & Sarah Vacle & Maria J. Marcaida & Matteo Dal Peraro, 2024. "Context-aware geometric deep learning for protein sequence design," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  16. Meghana Kshirsagar & Artur Meller & Ian R. Humphreys & Samuel Sledzieski & Yixi Xu & Rahul Dodhia & Eric Horvitz & Bonnie Berger & Gregory R. Bowman & Juan Lavista Ferres & David Baker & Minkyung Baek, 2025. "Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  17. Laura Shub & Wenjin Liu & Georgios Skiniotis & Michael J. Keiser & Michael J. Robertson, 2025. "MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  18. Gi Bae Kim & Ha Rim Kim & Sang Yup Lee, 2025. "Comprehensive evaluation of the capacities of microbial cell factories," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
  19. William Mo & Christopher A. Vaiana & Chris J. Myers, 2024. "The need for adaptability in detection, characterization, and attribution of biosecurity threats," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
  20. Chloe S. Adams & Hyojin Kim & Abigail E. Burtner & Dong Sun Lee & Craig Dobbins & Cameron Criswell & Brian Coventry & Adri Tran-Pearson & Ho Min Kim & Neil P. King, 2025. "De novo design of protein minibinder agonists of TLR3," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  21. Yash Chainani & Jacob Diaz & Margaret Guilarte-Silva & Vincent Blay & Quan Zhang & William Sprague & Keith E. J. Tyo & Linda J. Broadbelt & Aindrila Mukhopadhyay & Jay D. Keasling & Hector Garcia Mart, 2025. "Merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  22. Enrico Orsi & Lennart Schada von Borzyskowski & Stephan Noack & Pablo I. Nikel & Steffen N. Lindner, 2024. "Automated in vivo enzyme engineering accelerates biocatalyst optimization," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  23. Aika Iwama & Ryoji Kise & Hiroaki Akasaka & Fumiya K. Sano & Hidetaka S. Oshima & Asuka Inoue & Wataru Shihoya & Osamu Nureki, 2024. "Structure and dynamics of the pyroglutamylated RF-amide peptide QRFP receptor GPR103," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  24. Sophia Vincoff & Shrey Goel & Kseniia Kholina & Rishab Pulugurta & Pranay Vure & Pranam Chatterjee, 2025. "FusOn-pLM: a fusion oncoprotein-specific language model via adjusted rate masking," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
  25. Simeon D. Castle & Michiel Stock & Thomas E. Gorochowski, 2024. "Engineering is evolution: a perspective on design processes to engineer biology," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  26. Adibvafa Fallahpour & Vincent Gureghian & Guillaume J. Filion & Ariel B. Lindner & Amir Pandi, 2025. "CodonTransformer: a multispecies codon optimizer using context-aware neural networks," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  27. Ying Huang & Chenyang Xue & Ruiqian Bu & Cang Wu & Jiachen Li & Jinqiu Zhang & Jinyu Chen & Zhaoying Shi & Yonglong Chen & Yong Wang & Zhongmin Liu, 2024. "Inhibition and transport mechanisms of the ABC transporter hMRP5," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  28. Chase R. Freschlin & Sarah A. Fahlberg & Pete Heinzelman & Philip A. Romero, 2024. "Neural network extrapolation to distant regions of the protein fitness landscape," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  29. Sri Karthika Shanmugam & Scott A. Kanner & Xinle Zou & Enoch Amarh & Papiya Choudhury & Rajesh Soni & Robert S. Kass & Henry M. Colecraft, 2025. "Decoding polyubiquitin regulation of KV7. 1 (KCNQ1) surface expression with engineered linkage-selective deubiquitinases," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
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