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Protein diffusion models have emerged as a promising approach for protein design.
The Protein Data Bank
Helen M Berman, Tammy Battistuz, Talapady N Bhat, Wolfgang F Bluhm, Philip E Bourne, Kyle Burkhardt, Zukang Feng, Gary L Gilliland, Lisa Iype, Shri Jain, et al · 2002
Earlier work this paper cites.
Inhibiting the p53–MDM2 interaction: an important target for cancer therapy
Patrick Chène · 2003
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A closed compact structure of native Ca(2+)-calmodulin
Jennifer L Fallon and Florante A Quiocho · 2003
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Scoring function for automated assessment of protein structure template quality
Yang Zhang and Jeffrey Skolnick · 2004
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TM-align: a protein structure alignment algorithm based on the TM-score
Yang Zhang and Jeffrey Skolnick · 2005
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How significant is a protein structure similarity with TM-score= 0.5?
Jinrui Xu and Yang Zhang · 2010
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Correlation of in situ mechanosensitive responses of the Moraxella catarrhalis adhesin UspA1 with fibronectin and receptor CEACAM1 binding
Christopher Agnew, Elena Borodina, Nathan R Zaccai, Rebecca Conners, Nicholas M Burton, James A Vicary, David K Cole, Massimo Antognozzi, Mumtaz Virji, and R Leo Brady · 2011
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Adam: A method for stochastic optimization
Diederik P Kingma and Jimmy Ba · 2014
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Neural machine translation in linear time
Nal Kalchbrenner, Lasse Espeholt, Karen Simonyan, Aaron van den Oord, Alex Graves, and Koray Kavukcuoglu · 2016
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PyTorch Lightning, March 2019
William Falcon and The PyTorch Lightning team · 2019
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De novo design of potent and selective mimics of IL-2 and IL-15
Daniel-Adriano Silva, Shawn Yu, Umut Y Ulge, Jamie B Spangler, Kevin M Jude, Carlos Labão-Almeida, Lestat R Ali, Alfredo Quijano-Rubio, Mikel Ruterbusch, Isabel Leung, et al · 2019
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De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
Longxing Cao, Inna Goreshnik, Brian Coventry, James Brett Case, Lauren Miller, Lisa Kozodoy, Rita E Chen, Lauren Carter, Alexandra C Walls, Young-Jun Park, et al · 2020
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Denoising diffusion probabilistic models
Jonathan Ho, Ajay Jain, and Pieter Abbeel · 2020
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Score-based generative modeling through stochastic differential equations
Yang Song, Jascha Sohl-Dickstein, Diederik P Kingma, Abhishek Kumar, Stefano Ermon, and Ben Poole · 2020
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Accurate prediction of protein structures and interactions using a three-track neural network
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer, et al · 2021
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Computational design of a synthetic PD-1 agonist
Cassie M Bryan, Gabriel J Rocklin, Matthew J Bick, Alex Ford, Sonia Majri-Morrison, Ashley V Kroll, Chad J Miller, Lauren Carter, Inna Goreshnik, Alex Kang, et al · 2021
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Highly accurate protein structure prediction with AlphaFold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, et al · 2021
Cited alongside, same era.
De novo design of modular and tunable protein biosensors
Alfredo Quijano-Rubio, Hsien-Wei Yeh, Jooyoung Park, Hansol Lee, Robert A Langan, Scott E Boyken, Marc J Lajoie, Longxing Cao, Cameron M Chow, Marcos C Miranda, Jimin Wi, Hyo Jeong Hong, Lance Stewart, Byung-Ha Oh, and David Baker · 2021
Cited alongside, same era.
Bottom-up de novo design of functional proteins with complex structural features
Che Yang, Fabian Sesterhenn, Jaume Bonet, Eva A van Aalen, Leo Scheller, Luciano A Abriata, Johannes T Cramer, Xiaolin Wen, Stéphane Rosset, Sandrine Georgeon, et al · 2021
Cited alongside, same era.
Protein structure and sequence generation with equivariant denoising diffusion probabilistic models
Namrata Anand and Tudor Achim · 2022
Cited alongside, same era.
De novo metalloprotein design
Matthew J Chalkley, Samuel I Mann, and William F DeGrado · 2022
Uniprot: the universal protein knowledgebase in 2023
The UniProt Consortium · 2023
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Allan dos Santos Costa, Ilan Mitnikov, Mario Geiger, Manvitha Ponnapati, Tess Smidt, and Joseph Jacobson · 2023
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Kieran Didi, Francisco Vargas, Simon V Mathis, Vincent Dutordoir, Emile Mathieu, Urszula J Komorowska, and Pietro Lio · 2023
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Engineering protein-based therapeutics through structural and chemical design
Sasha B Ebrahimi and Devleena Samanta · 2023
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Illuminating protein space with a programmable generative model
John B Ingraham, Max Baranov, Zak Costello, Karl W Barber, Wujie Wang, Ahmed Ismail, Vincent Frappier, Dana M Lord, Christopher Ng-Thow-Hing, Erik R Van Vlack, et al · 2023
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Cited alongside, same era.
Robust deep learning–based protein sequence design using ProteinMPNN
Justas Dauparas, Ivan Anishchenko, Nathaniel Bennett, Hua Bai, Robert J Ragotte, Lukas F Milles, Basile IM Wicky, Alexis Courbet, Rob J de Haas, Neville Bethel, et al · 2022
Cited alongside, same era.
Language models of protein sequences at the scale of evolution enable accurate structure prediction
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, et al · 2022
Cited alongside, same era.
Flow matching for generative modeling
Yaron Lipman, Ricky TQ Chen, Heli Ben-Hamu, Maximilian Nickel, and Matt Le · 2022
Cited alongside, same era.
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications
Anthony Marchand, Alexandra K Van Hall-Beauvais, and Bruno E Correia · 2022
Cited alongside, same era.
Interleukin-2 superkines by computational design
Junming Ren, Alexander E Chu, Kevin M Jude, Lora K Picton, Aris J Kare, Leon Su, Alejandra Montano Romero, Po-Ssu Huang, and K Christopher Garcia · 2022
Cited alongside, same era.
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem
Brian L Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, and Tommi Jaakkola · 2022
Cited alongside, same era.
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, et al · 2022
Cited alongside, same era.
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Generating novel, designable, and diverse protein structures by equivariantly diffusing oriented residue clouds
Yeqing Lin and Mohammed AlQuraishi · 2023
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Unlocking de novo antibody design with generative artificial intelligence
Amir Shanehsazzadeh, Sharrol Bachas, Matt McPartlon, George Kasun, John M Sutton, Andrea K Steiger, Richard Shuai, Christa Kohnert, Goran Rakocevic, Jahir M Gutierrez, et al · 2023
Later among the works it cites.
De novo design of protein structure and function with RFdiffusion
Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, et al · 2023
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Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, and Tommi Jaakkola · 2024
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Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning
Karla M Castro, Joseph L Watson, Jue Wang, Joshua Southern, Reyhaneh Ayardulabi, Sandrine Georgeon, Stephane Rosset, David Baker, and Bruno E Correia · 2024
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A latent diffusion model for protein structure generation
Cong Fu, Keqiang Yan, Limei Wang, Wing Yee Au, Michael Curtis McThrow, Tao Komikado, Koji Maruhashi, Kanji Uchino, Xiaoning Qian, and Shuiwang Ji · 2024
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Blueprinting extendable nanomaterials with standardized protein blocks
Timothy F Huddy, Yang Hsia, Ryan D Kibler, Jinwei Xu, Neville Bethel, Deepesh Nagarajan, Rachel Redler, Philip JY Leung, Connor Weidle, Alexis Courbet, et al · 2024
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Fast and accurate protein structure search with Foldseek
Michel Van Kempen, Stephanie S Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron LM Gilchrist, Johannes Söding, and Martin Steinegger · 2024
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Proteus: exploring protein structure generation for enhanced designability and efficiency
Chentong Wang, Yannan Qu, Zhangzhi Peng, Yukai Wang, Hongli Zhu, Dachuan Chen, and Longxing Cao · 2024
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Improved motif-scaffolding with SE(3) flow matching
Jason Yim, Andrew Campbell, Emile Mathieu, Andrew YK Foong, Michael Gastegger, José Jiménez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S Veeling, Frank Noé, et al · 2024
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