ColabFold - Making protein folding accessible to all

Cited by (1,085)

Items 201–300 of 1,085

1. What does AlphaFold3 learn about antibody and nanobody docking, and what remains unsolved?
   Fatima N. Hitawala, Jeffrey J. Gray · 2025 · mAbs
2. EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
   Roche, Rahmatullah, Moussad, Bernard, Shuvo, Md Hossain, Tarafder, Sumit, Bhattacharya, Debswapna · 2024 · Nucleic Acids Research
3. Function of ceramide transfer protein for biogenesis and sphingolipid composition of extracellular vesicles
   Simone M. Crivelli, Caterina Giovagnoni, Zhihui Zhu, Priyanka Tripathi, Ahmed M. Elsherbini, Zainuddin Quadri, Jian Yu Pu, Liping Zhang, Branislav Ferko, Dušan Berkeš et al. · 2022 · Journal of Extracellular Vesicles
4. Structural analysis and architectural principles of the bacterial amyloid curli
   Mike Sleutel, Brajabandhu Pradhan, Alexander N. Volkov, Han K. Remaut · 2023 · Nature Communications
5. CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2
   Shor, Ben, Schneidman-Duhovny, Dina · 2024 · Nature Methods
6. A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers
   Mohammed Khaled, Isabel Rönnbäck, Leopold L. Ilag, Astrid Gräslund, Birgit Strodel, Nicklas Österlund · 2023 · Journal of the American Chemical Society
7. A non‐canonical scaffold‐type E3 ligase complex mediates protein UFMylation
   Joshua J. Peter, H Magnussen, Paul A. DaRosa, David Millrine, Stephen P. Matthews, Frédéric Lamoliatte, Ramasubramanian Sundaramoorthy, Ron R. Kopito, Yogesh Kulathu · 2022 · The EMBO Journal
8. IFT-A structure reveals carriages for membrane protein transport into cilia
   Hesketh, Sophie J., Mukhopadhyay, Aakash G., Nakamura, Dai, Toropova, Katerina, Roberts, Anthony J. · 2022 · Cell
9. An E1–E2 fusion protein primes antiviral immune signalling in bacteria
   Ledvina, Hannah E., Ye, Qiaozhen, Gu, Yajie, Sullivan, Ashley E., Quan, Yun, Lau, Rebecca K., Zhou, Huilin, Corbett, Kevin D., Whiteley, Aaron T. · 2023 · Nature
10. Hybrids of RNA viruses and viroid-like elements replicate in fungi
    Marco Forgia, Beatriz Navarro, Stefania Daghino, Amelia Cervera, Andreas Gisel, Silvia Perotto, Dilzara N. Aghayeva, Mary F. Akinyuwa, Emanuela Gobbi, Ivan N. Zheludev et al. · 2023 · Nature Communications
11. De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking
    Chen, Zhen, Shiozaki, Momoko, Haas, Kelsey M., Skinner, Will M., Zhao, Shumei, Guo, Caiying, Polacco, Benjamin J., Yu, Zhiheng, Krogan, Nevan J., Lishko, Polina V. et al. · 2023 · Cell
12. Structural principles of B cell antigen receptor assembly
    Dong, Ying, Pi, Xiong, Bartels-Burgahn, Frauke, Saltukoglu, Deniz, Liang, Zhuoyi, Yang, Jianying, Alt, Frederick W., Reth, Michael, Wu, Hao · 2022 · Nature
13. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein–protein interactions in the human cell
    Tara K. Bartolec, Xabier Vázquez-Campos, Alexander R. Norman, Clement Luong, Marcus Johnson, Richard J. Payne, Marc Ronald Wilkins, Joel P. Mackay, Jason K. K. Low · 2023 · Proceedings of the National Academy of Sciences
14. AlphaFold two years on: Validation and impact
    Oleg V. Kovalevskiy, Juan C Mateos-Garcia, Kathryn Tunyasuvunakool · 2024 · Proceedings of the National Academy of Sciences
15. De novo design of peptide binders to conformationally diverse targets with contrastive language modeling
    Suhaas Bhat, Kalyan Palepu, Lauren Hong, Yiwei Mao, Tianzheng Ye, Rema Iyer, Lin Zhao, Tianlai Chen, Sophia Vincoff, Rio Watson et al. · 2025 · Science Advances
16. Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties
    Sala, Davide, Hildebrand, Peter W., Meiler, Jens · 2023 · Frontiers in Molecular Biosciences
17. Peroxide-Mediated Oxygenation of Organic Compounds by Fungal Peroxygenases
    Martin Hofrichter, Harald Kellner, Robert Herzog, Alexander Karich, Jan Kiebist, Katrin Scheibner, René Ullrich · 2022 · Antioxidants
18. Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study
    Daniel J. Sheward, Changil Kim, Roy A. Ehling, Alec P. Pankow, Xaquín Castro Dopico, Robert Dyrdak, Darren Patrick Martin, Sai T. Reddy, Joakim Dillner, Gunilla B. Karlsson Hedestam et al. · 2022 · The Lancet Infectious Diseases
19. Arabidopsis immune responses triggered by cellulose‐ and mixed‐linked glucan‐derived oligosaccharides require a group of leucine‐rich repeat malectin receptor kinases
    Marina Martín‐Dacal, Patricia Fernández‐Calvo, Pedro Jiménez‐Sandoval, Gemma López, María Garrido‐Arandia, Diego Rebaque, Irene del Hierro, Diego José Berlanga, Miguel Ángel Medina Torres, Varun Kumar et al. · 2022 · The Plant Journal
20. Recent advances in predicting and modeling protein–protein interactions
    Jesse Durham, Jing Zhang, Ian R. Humphreys, Jimin Pei, Qian Cong · 2023 · Trends in Biochemical Sciences
21. The Troyer syndrome protein spartin mediates selective autophagy of lipid droplets
    Jeeyun Chung, Joongkyu Park, Zon Weng Lai, Talley J. Lambert, Ruth C. Richards, Jiuchun Zhang, Tobias C. Walther, Robert V. Farese · 2023 · Nature Cell Biology
22. Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress
    Mohamed A. Eldeeb, Andrew N. Bayne, Armaan Fallahi, Thomas Goiran, Emma J. MacDougall, Andrea Soumbasis, Cornelia E. Zorca, Jace Jones-Tabah, Rhalena A. Thomas, Nathan C. Karpilovsky et al. · 2024 · Proceedings of the National Academy of Sciences
23. Direct optical measurement of intramolecular distances with angstrom precision
    Steffen J. Sahl, Jessica Matthias, Kaushik Inamdar, Michael Weber, Taukeer A. Khan, Christian Brüser, Stefan Jakobs, Stefan Becker, Christian Griesinger, Johannes Broichhagen et al. · 2024 · Science
24. Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
    Liam James McGuffin, Nicholas S. Edmunds, Ahmet G Genc, Shuaa M. A. Alharbi, Bajuna R. Salehe, Recep Adiyaman · 2023 · Nucleic Acids Research
25. FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors
    Giang Nguyen, Keri‐Lyn Kozul, Yi Cui, Brendan Townsend, Prajakta Gosavi, Soo Siang Ooi, Antonio Marzio, Nissa L. Carrodus, Steven Zuryn, Michele Pagano et al. · 2023 · The EMBO Journal
26. Cas12n nucleases, early evolutionary intermediates of type V CRISPR, comprise a distinct family of miniature genome editors
    Weizhong Chen, Jiacheng Ma, Zhaowei Wu, Zhipeng Wang, Hongyuan Zhang, Wenhan Fu, Deng Pan, Shi Kun Jin, Quanjiang Ji · 2023 · Molecular Cell
27. Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
    Marc Ferdinand Lensink, Guillaume Brysbaert, Nessim RAOURAOUA, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato, Charlotte W. van Noort, João M. C. Teixeira, Alexandre M. J. J. Bonvin, Ren Kong et al. · 2023 · Proteins Structure Function and Bioinformatics
28. TGF-β and RAS jointly unmask primed enhancers to drive metastasis
    Jun Ho Lee, Francisco J. Sánchez Rivera, Lan Ying He, Harihar Basnet, Fei Chen, Elena Spina, Liangji Li, Carles Torner, Jason Earl Chan, Dig Vijay Kumar Yarlagadda et al. · 2024 · Cell
29. Mapping the T cell repertoire to a complex gut bacterial community
    2023
30. A conserved fertilization complex bridges sperm and egg in vertebrates
    Deneke, Victoria E., Blaha, Andreas, Lu, Yonggang, Suwita, Johannes P., Draper, Jonne M., Phan, Clara S., Panser, Karin, Schleiffer, Alexander, Jacob, Laurine, Humer, Theresa et al. · 2024 · Cell
31. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
    Widen, Sonya A., Bes, Israel Campo, Koreshova, Alevtina, Pliota, Pinelopi, Krogull, Daniel, Burga, Alejandro · 2023 · Science
32. In Silico Repurposed Drugs against Monkeypox Virus
    Hilbert Yuen In Lam, Jia Sheng Guan, Yuguang Mu · 2022 · Molecules
33. Combinatorial assembly and design of enzymes
    Lipsh-Sokolik, R., Khersonsky, O., Schröder, S. P., de Boer, C., Hoch, S.-Y., Davies, G. J., Overkleeft, H. S., Fleishman, S. J. · 2023 · Science
34. Proteome census upon nutrient stress reveals Golgiphagy membrane receptors
    Kelsey L. Hickey, Sharan Swarup, Ian R.L. Smith, Julia C. Paoli, Enya Miguel Whelan, João A. Paulo, J. Wade Harper · 2023 · Nature
35. Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64
    Ruobing Wang, Anru Zhang, Shijun Sun, Guankun Yin, Xingyu Wu, Qi Ding, Qi Wang, Fengning Chen, Shuyi Wang, Lucy van Dorp et al. · 2024 · Nature Communications
36. Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements
    Florian Tesson, Erin D. Huiting, Linlin Wei, Jie Ren, Matthew Johnson, Rémi Planel, Jean Cury, Yue Feng, Joseph Bondy‐Denomy, Aude G. Bernheim · 2024 · Nucleic Acids Research
37. Bat genomes illuminate adaptations to viral tolerance and disease resistance
    Morales, Ariadna E., Dong, Yue, Brown, Thomas, Baid, Kaushal, Kontopoulos, Dimitrios - Georgios, Gonzalez, Victoria, Huang, Zixia, Ahmed, Alexis-Walid, Bhuinya, Arkadeb, Hilgers, Leon et al. · 2025 · Nature
38. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor-binding domain
    K. Nabel, S. Clark, S. Shankar, Junhua Pan, L. Clark, Pan Yang, A. Coscia, Lindsay G. A. McKay, Haley Varnum, Vesna Brusic et al. · 2021 · Science
39. RNA-activated protein cleavage with a CRISPR-associated endopeptidase
    Jonathan G. Strecker, F. Esra Demircioglu, David Li, Guilhem Faure, Max E. Wilkinson, Jonathan S. Gootenberg, Omar O. Abudayyeh, Hiroshi Nishimasu, Rhiannon K. Macrae, Feng Zhang · 2022 · Science
40. De novo-designed pMHC binders facilitate T cell–mediated cytotoxicity toward cancer cells
    Johansen, Kristoffer Haurum, Wolff, Darian Stephan, Scapolo, Beatrice, Fernández-Quintero, Monica L., Risager Christensen, Charlotte, Loeffler, Johannes R., Rivera-de-Torre, Esperanza, Overath, Max D., Kjærgaard Munk, Kamilla, Morell, Oliver et al. · 2025 · Science
41. A De Novo Metalloenzyme for Cerium Photoredox Catalysis
    2024
42. Genome-wide screen reveals Rab12 GTPase as a critical activator of Parkinson’s disease-linked LRRK2 kinase
    Dhekne, Herschel S, Tonelli, Francesca, Yeshaw, Wondwossen M, Chiang, Claire Y, Limouse, Charles, Jaimon, Ebsy, Purlyte, Elena, Alessi, Dario R, Pfeffer, Suzanne R · 2023 · eLife
43. Building structural models of a whole mycoplasma cell
    Maritan, Martina, Autin, Ludovic, Karr, Jonathan, Covert, Markus W., Olson, Arthur J., Goodsell, David S. · 2022 · Journal of Molecular Biology
44. Accurate protein structure prediction: what comes next?
    Chaok Seok, Minkyung Baek, Martin Steinegger, Hahnbeom Park, Gyu Rie Lee, Jonghun Won · 2021 · Korean Society for Structural Biology
45. Rapid and sensitive protein complex alignment with Foldseek-Multimer
    Woosub Kim, Milot Mirdita, Eli Levy Karin, Cameron L. M. Gilchrist, Hugo Schweke, Johannes Söding, Emmanuel D. Levy, Martin Steinegger · 2025 · Nature Methods
46. Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer
    Ah‐Ram Kim, Yanhui Hu, Aram Comjean, Jonathan Rodiger, Stephanie Elizabeth Mohr, Norbert Perrimon · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
47. Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids
    2023
48. Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis
    Tingting Lou, Annan Li, Houchao Xu, Jingfeng Pan, Baiying Xing, Ruibo Wu, Jeroen S. Dickschat, Donghui Yang, Ming Ma · 2023 · Journal of the American Chemical Society
49. Diversity, evolution, and classification of the RNA-guided nucleases TnpB and Cas12
    Han Altae-Tran, Sergey Shmakov, Kira S. Makarova, Yuri I. Wolf, Soumya Kannan, Feng Zhang, Eugene V. Koonin · 2023 · Proceedings of the National Academy of Sciences
50. Activation of Thoeris antiviral system via SIR2 effector filament assembly
    Giedrė Tamulaitienė, Dziugas Sabonis, Giedrius Sasnauskas, Audronė Rukšėnaitė, Arūnas Šilanskas, Carmel Avraham, Gal Ofir, Rotem Sorek, Mindaugas Zaremba, Virginijus Šikšnys · 2024 · Nature
51. Cryo-EM and artificial intelligence visualize endogenous protein community members
    Skalidis, Ioannis, Kyrilis, Fotis L., Tüting, Christian, Hamdi, Farzad, Chojnowski, Grzegorz, Kastritis, Panagiotis L. · 2022 · Structure
52. Viroid-like colonists of human microbiomes
    Zheludev, Ivan N., Edgar, Robert C., Lopez-Galiano, Maria Jose, de la Peña, Marcos, Babaian, Artem, Bhatt, Ami S., Fire, Andrew Z. · 2024 · Cell
53. TransDTI: Transformer-Based Language Models for Estimating DTIs and Building a Drug Recommendation Workflow
    Yogesh Kalakoti, Shashank Yadav, Durai Sundar · 2022 · ACS Omega
54. Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex
    Julian F. Ehrmann, Daniel B. Grabarczyk, Maria Heinke, Luiza Deszcz, R Kurzbauer, Otto Hudecz, Alexandra Shulkina, Rebeca Gogova, Anton Meinhart, Gijs A. Versteeg et al. · 2023 · Science
55. Updated protein domain annotation of the PARP protein family sheds new light on biological function
    Marcin J. Suskiewicz, Deeksha Munnur, Øyvind Strømland, Ji-Chun Yang, Laura E. Easton, Chatrin Chatrin, Kang Zhu, Domagoj Baretić, Stéphane Goffinont, Marion Schuller et al. · 2023 · Nucleic Acids Research
56. Monomerization of TDP-43 is a key determinant for inducing TDP-43 pathology in amyotrophic lateral sclerosis
    Kotaro Oiwa, Seiji Watanabe, Kazunari Onodera, Yohei Iguchi, Yukako Kinoshita, Okiru Komine, Akira Sobue, Yohei Okada, Masahisa Katsuno, Koji Yamanaka · 2023 · Science Advances
57. De novo design of drug-binding proteins with predictable binding energy and specificity
    Lei Lü, Xuxu Gou, Sophia K. Tan, Samuel I. Mann, Hyunjun Yang, Xiaofang Zhong, Dimitris Gazgalis, Jesús Valdiviezo, Hyunil Jo, Yibing Wu et al. · 2024 · Science
58. A family of NADPH/NADP+ biosensors reveals in vivo dynamics of central redox metabolism across eukaryotes
    Marie Scherschel, Jan-Ole Niemeier, Lianne H.C. Jacobs, Markus D. A. Hoffmann, Anika Diederich, Christopher Bell, Pascal Höhne, Sonja Raetz, Johanna B. Kroll, Janina Steinbeck et al. · 2024 · Nature Communications
59. A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth
    Marina R. Good, Monica L. Fernández‐Quintero, Wei Ji, Alesandra J. Rodriguez, Julianna Han, Andrew B. Ward, Jenna J. Guthmiller · 2024 · Nature Communications
60. Viroid-like colonists of human microbiomes
    Zheludev, Ivan N., Edgar, Robert C., Lopez-Galiano, Maria Jose, de la Peña, Marcos, Babaian, Artem, Bhatt, Ami S., Fire, Andrew Z. · 2024
61. Novel machine learning approaches revolutionize protein knowledge
    Bordin, Nicola, Dallago, Christian, Heinzinger, Michael, Kim, Stephanie, Littmann, Maria, Rauer, Clemens, Steinegger, Martin, Rost, Burkhard, Orengo, Christine · 2023 · Trends in Biochemical Sciences
62. Molecular pathway of mitochondrial preprotein import through the TOM–TIM23 supercomplex
    Zhou, Xueyin, Yang, Yuqi, Wang, Guopeng, Wang, Shanshan, Sun, Dongjie, Ou, Xiaomin, Lian, Yuke, Li, Long · 2023 · Nature Structural & Molecular Biology
63. Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem
    Rob J. M. van Spanning, Qingtian Guan, Chrats Melkonian, James Gallant, Lùbos Polerecký, Jean‐François Flot, Bernd Willem Brandt, Martin Braster, Paul Iturbe-Espinoza, Joost W. Aerts et al. · 2022 · Nature Microbiology
64. Inositol pyrophosphate dynamics reveals control of the yeast phosphate starvation program through 1,5-IP8 and the SPX domain of Pho81
    Valentin Chabert, Geun-Don Kim, Danye Qiu, Guizhen Liu, Lydie Michaillat Mayer, Muhammed Jamsheer K, Henning Jacob Jessen, Andreas Mayer · 2023 · eLife
65. Plant carbonic anhydrase-like enzymes in neuroactive alkaloid biosynthesis
    Ryan S. Nett, Yaereen Dho, Chun J. Tsai, Daria Passow, Jaime E. Martinez Grundman, Yun‐Yee Low, Elizabeth S. Sattely · 2023 · Nature
66. Structural basis of Integrator-dependent RNA polymerase II termination
    Isaac Fianu, Moritz Ochmann, James L. Walshe, Olexandr Dybkov, Joseph Neos Cruz, Henning Urlaub, Patrick Cramer · 2024 · Nature
67. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9
    Amy R. Eggers, Kai Chen, Katarzyna M. Soczek, Owen T. Tuck, Erin E. Doherty, Bryant Xu, Marena I. Trinidad, Brittney W. Thornton, Peter H. Yoon, Jennifer A. Doudna · 2024 · Cell
68. Protein structure-informed bacteriophage genome annotation with Phold
    Bouras, George, Grigson, Susanna R, Mirdita, Milot, Heinzinger, Michael, Papudeshi, Bhavya, Mallawaarachchi, Vijini, Green, Renee, Kim, Rachel Seongeun, Mihalia, Victor, Psaltis, Alkis James et al. · 2026 · Nucleic Acids Research
69. GPU-accelerated homology search with MMseqs2
    2025
70. Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility
    Stallmeyer, Birgit, Bühlmann, Clara, Stakaitis, Rytis, Dicke, Ann-Kristin, Ghieh, Farah, Meier, Luisa, Zoch, Ansgar, MacKenzie MacLeod, David, Steingröver, Johanna, Okutman, Özlem et al. · 2024 · Nature Communications
71. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
    Shoshana J. Wodak, Sándor Vajda, Marc Ferdinand Lensink, Dima Kozakov, Paul A. Bates · 2023 · Annual Review of Biophysics
72. Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products
    Adam M. Bayless, Sisi Chen, Sam C. Ogden, Xiaoyan Xu, John D. Sidda, Mohammad Kawsar Manik, Sulin Li, Boštjan Kobe, Thomas Ve, Lijiang Song et al. · 2023 · Science Advances
73. An Epstein-Barr virus protein interaction map reveals NLRP3 inflammasome evasion via MAVS UFMylation
    Stephanie Pei Tung Yiu, Cassie M. Zerbe, David Vanderwall, Edward L. Huttlin, Michael P. Weekes, Benjamin E. Gewurz · 2023 · Molecular Cell
74. Sensitive multicolor indicators for monitoring norepinephrine in vivo
    Zacharoula Kagiampaki, Valentin Rohner, Cedric Kiss, Sebastiano Curreli, Alexander Dieter, Maria Wilhelm, Masaya Harada, Sian N. Duss, Jan Dernič, Musadiq Ahmad Bhat et al. · 2023 · Nature Methods
75. Deep learning for protein structure prediction and design—progress and applications
    Jürgen Jänes, Pedro Beltrão · 2024 · Molecular Systems Biology
76. Mapping glycoprotein structure reveals Flaviviridae evolutionary history
    Jonathon C. O. Mifsud, Spyros Lytras, Michael R. Oliver, Kamilla Toon, Vincenzo A. Costa, Edward Charles Holmes, Joe Grove · 2024 · Nature
77. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins
    Noureddine Lazar, Carl H. Mesarich, Yohann Petit, Nacèra Talbi, I. Li de la Sierra-Gallay, Emilie Zélie, Karine Blondeau, Jérôme Gracy, Bénédicte Ollivier, Françoise Blaise et al. · 2022 · PLoS Pathogens
78. One bead per residue can describe all-atom protein structures
    Lim Heo, Michael Feig · 2023 · Structure
79. Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics
    Joshua B. Simpson, Morgan E. Walker, Josh J. Sekela, Samantha M. Ivey, Parth B. Jariwala, Cameron M. Storch, Mark E. Kowalewski, Amanda L. Graboski, Adam D. Lietzan, William G. Walton et al. · 2024 · Cell Host & Microbe
80. Emergence of a distinct mechanism of C–N bond formation in photoenzymes
    Felix C. Raps, Ariadna Rivas-Souchet, Chey M. Jones, Todd K. Hyster · 2024 · Nature
81. NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation
    Kagaya, Yuki, Zhang, Zicong, Ibtehaz, Nabil, Wang, Xiao, Nakamura, Tsukasa, Punuru, Pranav Deep, Kihara, Daisuke · 2025 · Nature Communications
82. Machine learning prediction of enzyme optimum pH
    Japheth E. Gado, Matthew Knotts, Ada Y. Shaw, Debora S. Marks, Nicholas Paul Gauthier, Chris Sander, Gregg T. Beckham · 2025 · Nature Machine Intelligence
83. High-throughput PRIME-editing screens identify functional DNA variants in the human genome
    Ren, Xingjie, Yang, Han, Nierenberg, Jovia L., Sun, Yifan, Chen, Jiawen, Beaman, Cooper, Pham, Thu, Nobuhara, Mai, Takagi, Maya Asami, Narayan, Vivek et al. · 2023 · Molecular Cell
84. A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin
    Qiu, Deyun, Pei, Jinxin V., Rosling, James E. O., Thathy, Vandana, Li, Dongdi, Xue, Yi, Tanner, John D., Penington, Jocelyn Sietsma, Aw, Yi Tong Vincent, Aw, Jessica Yi Han et al. · 2022 · Nature Communications
85. Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
    Foley, Gabriel, Mora, Ariane, Ross, Connie M., Bottoms, Scott, Sützl, Leander, Lamprecht, Marnie L., Zaugg, Julian, Essebier, Alexandra, Balderson, Brad, Newell, Rhys et al. · 2022 · PLOS Computational Biology
86. Structure of an endogenous mycobacterial MCE lipid transporter
    Chen, James, Fruhauf, Alice, Fan, Catherine, Ponce, Jackeline, Ueberheide, Beatrix, Bhabha, Gira, Ekiert, Damian C. · 2023 · Nature
87. Self-play reinforcement learning guides protein engineering
    Yi Wang, Hui Tang, Lichao Huang, Lulu Pan, Lixiang Yang, Huanming Yang, Feng Mu, Meng Yang · 2023 · Nature Machine Intelligence
88. Bacterial pathogens deliver water- and solute-permeable channels to plant cells
    Kinya Nomura, Felipe Andreazza, Jie Cheng, Ke Dong, Pei Zhou, Sheng Yang He · 2023 · Nature
89. Jasmonate signaling pathway confers salt tolerance through a NUCLEAR FACTOR-Y trimeric transcription factor complex in Arabidopsis
    Xing Li, Changjiang Li, Lei Shi, Gaofeng Lv, Xi Li, Yixuan Liu, Xiaojie Jia, Jiyuan Liu, Yuqian Chen, Lei Zhu et al. · 2024 · Cell Reports
90. AlphaFold-guided redesign of a plant pectin methylesterase inhibitor for broad-spectrum disease resistance
    Yeqiang Xia, Guangzheng Sun, Jun‐Hua Xiao, Xinyi He, Haibin Jiang, Zhichao Zhang, Qi Zhang, Kainan Li, Sicong Zhang, Xuechao Shi et al. · 2024 · Molecular Plant
91. Strengthening nucleic acid biosecurity screening against generative protein design tools
    Bruce J. Wittmann, Tessa Alexanian, Craig M. Bartling, Jacob Beal, Adam J. Clore, James Diggans, Kevin Flyangolts, Bryan T. Gemler, Tom Mitchell, Steven T. Murphy et al. · 2025 · Science
92. Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro
    Ghani, Usman, Desta, Israel, Jindal, Akhil, Khan, Omeir, Jones, George, Hashemi, Nasser, Kotelnikov, Sergey, Padhorny, Dzmitry, Vajda, Sandor, Kozakov, Dima · 2021
93. Stress-dependent cell stiffening by tardigrade tolerance proteins that reversibly form a filamentous network and gel
    Akihiro Tanaka, Tomomi Nakano, Kento Watanabe, Kazutoshi Masuda, Gen Honda, Shuichi Kamata, Reitaro Yasui, Hiroko Kozuka‐Hata, Chiho WATANABE, Takumi Chinen et al. · 2022 · PLoS Biology
94. Bacterial Cytochrome P450 Catalyzed Post‐translational Macrocyclization of Ribosomal Peptides**
    Bei‐Bei He, Jing Liu, Zhuo Cheng, Runze Liu, Zheng Zhong, Ying Gao, Hongyan Liu, Zhi‐Man Song, Yongqi Tian, Yong‐Xin Li · 2023 · Angewandte Chemie International Edition
95. Molecular mechanism of dynein-dynactin complex assembly by LIS1
    Kashish Singh, Clinton K. Lau, Giulia Manigrasso, José B. Gama, Reto Gassmann, Andrew P. Carter · 2024 · Science
96. Architecture and activation mechanism of the bacterial PARIS defence system
    Amar Deep, Qishan Liang, Eray Enüstün, Joe Pogliano, Kevin D. Corbett · 2024 · Nature
97. Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
    Laso-Pérez, Rafael, Wu, Fabai, Crémière, Antoine, Speth, Daan R., Magyar, John S., Zhao, Kehan, Krupovic, Mart, Orphan, Victoria J. · 2023 · Nature Microbiology
98. Deep learning–guided design of dynamic proteins
    Guo, Amy B., Akpinaroglu, Deniz, Stephens, Christina A., Grabe, Michael, Smith, Colin A., Kelly, Mark J. S., Kortemme, Tanja · 2025 · Science
99. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense
    Zhifeng Zeng, Yu Chen, Rafael Pinilla‐Redondo, Shiraz Ali Shah, Fen Zhao, Chen Wang, Zeyu Hu, Chang Guang Wu, Changyi Zhang, Rachel J. Whitaker et al. · 2022 · Cell Host & Microbe
100. Structure of the rabies virus glycoprotein trimer bound to a prefusion-specific neutralizing antibody
     Heather Callaway, Dawid S. Zyla, Florence Larrous, Guilherme Dias de Melo, Kathryn M. Hastie, Rubén Díaz-Avalos, Alyssa Agarwal, Davide Corti, Hervé Bourhy, Erica Ollmann Saphire · 2022 · Science Advances