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Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes.
Principles that govern the folding of protein chains
Christian B Anfinsen · 1973
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Sequential Monte Carlo Methods in Practice , volume 1
Arnaud Doucet, Nando De Freitas, and Neil James Gordon · 2001
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Central limit theorem for sequential Monte Carlo methods and its application to Bayesian inference
Nicolas Chopin · 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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MaxCluster: a tool for protein structure comparison and clustering
Alex Herbert and MJE Sternberg · 2008
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De novo computational design of retro-aldol enzymes
Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas III, Donald Hilvert, Kendal N Houk, Barry L. Stoddard, and David Baker · 2008
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A tutorial on particle filtering and smoothing: Fifteen years later
Arnaud Doucet and Adam M Johansen · 2009
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Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
Justin B Siegel, Alexandre Zanghellini, Helena M Lovick, Gert Kiss, Abigail R Lambert, Jennifer L StClair, Jasmine L Gallaher, Donald Hilvert, Michael H Gelb, Barry L Stoddard, Kendall N Houk, Forrest E Michael, and David Baker · 2010
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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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Rosettascripts: a scripting language interface to the Rosetta macromolecular modeling suite
Sarel J Fleishman, Andrew Leaver-Fay, Jacob E Corn, Eva-Maria Strauch, Sagar D Khare, Nobuyasu Koga, Justin Ashworth, Paul Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, and David Baker · 2011
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Accessing protein conformational ensembles using room-temperature x-ray crystallography
James S Fraser, Henry van den Bedem, Avi J Samelson, P Therese Lang, James M Holton, Nathaniel Echols, and Tom Alber · 2011
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Computational design of self-assembling protein nanomaterials with atomic level accuracy
Neil P King, William Sheffler, Michael R Sawaya, Breanna S Vollmar, John P Sumida, Ingemar André, Tamir Gonen, Todd O Yeates, and David Baker · 2012
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Proof of principle for epitope-focused vaccine design
Bruno E Correia, John T Bates, Rebecca J Loomis, Gretchen Baneyx, Chris Carrico, Joseph G Jardine, Peter Rupert, Colin Correnti, Oleksandr Kalyuzhniy, Vinayak Vittal, Mary J Connell, Eric Stevens, Alexandria Schroeter, Man Chen, Skye Macpherson, Andreia M Serra, Yumiko Adachi, Margaret A Holmes, Yuxing Li, Rachel E Klevit, Barney S Graham, Richard T Wyatt, David Baker, Roland K Strong, James E Crowe, Jr, Philip R Johnson, and William R Schief · 2014
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Fast protein folding kinetics
Hannah Gelman and Martin Gruebele · 2014
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A computationally designed inhibitor of an Epstein-Barr viral BCL-2 protein induces apoptosis in infected cells
Erik Procko, Geoffrey Y Berguig, Betty W Shen, Yifan Song, Shani Frayo, Anthony J Convertine, Daciana Margineantu, Garrett Booth, Bruno E Correia, Yuanhua Cheng, William R Schief, David M Hockenbery, Oliver W Press, Barry L Stoddard, Patrick S Stayton, and David Baker · 2014
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Deep unsupervised learning using nonequilibrium thermodynamics
Jascha Sohl-Dickstein, Eric Weiss, Niru Maheswaranathan, and Surya Ganguli · 2015
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Motif-driven design of protein–protein interfaces
Daniel-Adriano Silva, Bruno E Correia, and Erik Procko · 2016
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
Cited alongside, same era.
Generative modeling for protein structures
Namrata Anand and Possu Huang · 2018
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Generative models for graph-based protein design
John Ingraham, Vikas Garg, Regina Barzilay, and Tommi Jaakkola · 2019
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An Introduction to Sequential Monte Carlo
Nicolas Chopin and Omiros Papaspiliopoulos · 2020
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Denoising diffusion probabilistic models
Jonathan Ho, Ajay Jain, and Pieter Abbeel · 2020
Cited alongside, same era.
De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Thomas W Linsky, Renan Vergara, Nuria Codina, Jorgen W Nelson, Matthew J Walker, Wen Su, Christopher O Barnes, Tien-Ying Hsiang, Katharina Esser-Nobis, Kevin Yu, Z Beau Reneer, Yixuan J Hou, Tanu Priya, Masaya Mitsumoto, Avery Pong, Uland Y Lau, Marsha L Mason, Jerry Chen, Alex Chen, Tania Berrocal, Hong Peng, Nicole S Clairmont, Javier Castellanos, Yu-Ru Lin, Anna Josephson-Day, Ralph S Baric, Deborah H Fuller, Carl D Walkey, Ted M Ross, Ryan Swanson, Pamela J Bjorkman, Michael Gale, Luis M Blancas-Mejia, Hui-Ling Yen, and Daniel-Adriano Silva · 2020
3D shape generation and completion through point-voxel diffusion
Linqi Zhou, Yilun Du, and Jiajun Wu · 2021
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Protein structure and sequence generation with equivariant denoising diffusion probabilistic models
Namrata Anand and Tudor Achim · 2022
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E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials
Simon Batzner, Albert Musaelian, Lixin Sun, Mario Geiger, Jonathan P Mailoa, Mordechai Kornbluth, Nicola Molinari, Tess E Smidt, and Boris Kozinsky · 2022
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Improving de novo protein binder design with deep learning
Nathaniel Bennett, Brian Coventry, Inna Goreshnik, Buwei Huang, Aza Allen, Dionne Vafeados, Ying Po Peng, Justas Dauparas, Minkyung Baek, Lance Stewart, , Frank DiMaio, Steven De Munck, Savvas N. Savvides, and David Baker · 2022
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Design of protein binding proteins from target structure alone
Longxing Cao, Brian Coventry, Inna Goreshnik, Buwei Huang, Joon Sung Park, Kevin M Jude, Iva Marković, Rameshwar U Kadam, Koen H G Verschueren, Kenneth Verstraete, Scott Thomas Russell Walsh, Nathaniel Bennett, Ashish Phal, Aerin Yang, Lisa Kozodoy, Michelle DeWitt, Lora Picton, Lauren Miller, Eva-Maria Strauch, Nicholas D DeBouver, Allison Pires, Asim K Bera, Samer Halabiya, Bradley Hammerson, Wei Yang, Steffen Bernard, Lance Stewart, Ian A Wilson, Hannele Ruohola-Baker, Joseph Schlessinger, Sangwon Lee, Savvas N Savvides, K Christopher Garcia, and David Baker · 2022
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Cited alongside, same era.
De novo protein design enables the precise induction of RSV-neutralizing antibodies
Fabian Sesterhenn, Che Yang, Jaume Bonet, Johannes T Cramer, Xiaolin Wen, Yimeng Wang, Chi-I Chiang, Luciano A Abriata, Iga Kucharska, Giacomo Castoro, Sabrina S Vollers, Marie Galloux, Elie Dheilly, Stéphane Rosset, Patricia Corthésy, Sandrine Georgeon, Mélanie Villard, Charles-Adrien Richard, Delphyne Descamps, Teresa Delgado, Elisa Oricchio, Marie-Anne Rameix-Welti, Vicente Más, Sean Ervin, Jean-François Eléouët, Sabine Riffault, John T Bates, Jean-Philippe Julien, Yuxing Li, Theodore Jardetzky, Thomas Krey, and Bruno E Correia · 2020
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Design of proteins presenting discontinuous functional sites using deep learning
Doug Tischer, Sidney Lisanza, Jue Wang, Runze Dong, Ivan Anishchenko, Lukas F Milles, Sergey Ovchinnikov, and David Baker · 2020
Cited alongside, same era.
Increasing the efficiency and accuracy of the ABACUS protein sequence design method
Peng Xiong, Xiuhong Hu, Bin Huang, Jiahai Zhang, Quan Chen, and Haiyan Liu · 2020
Cited alongside, same era.
De novo protein design by deep network hallucination
Ivan Anishchenko, Samuel J Pellock, Tamuka M Chidyausiku, Theresa A Ramelot, Sergey Ovchinnikov, Jingzhou Hao, Khushboo Bafna, Christoffer Norn, Alex Kang, Asim K Bera, Frank DiMaio, Lauren Carter, Cameron M Chow, Gaetano T Montelione, and David Baker · 2021
Cited alongside, same era.
Highly accurate protein structure prediction with AlphaFold
John M. Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Zídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon A A Kohl, Andy Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David A. Reiman, Ellen Clancy, Michal Zielinski, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian Bodenstein, David Silver, Oriol Vinyals, Andrew W. Senior, Koray Kavukcuoglu, Pushmeet Kohli, and Demis Hassabis · 2021
Cited alongside, same era.
Variational diffusion models
Diederik Kingma, Tim Salimans, Ben Poole, and Jonathan Ho · 2021
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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, Phil J. Y. Leung, Tim F. Huddy, Sam Pellock, Doug Tischer, Frederick Chan, Brian Koepnick, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Asim K. Bera, Neil P. King, and David A. Baker · 2022
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ProtGPT2 is a deep unsupervised language model for protein design
Noelia Ferruz, Steffen Schmidt, and Birte Höcker · 2022
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Video diffusion models
Jonathan Ho, Tim Salimans, Alexey Gritsenko, William Chan, Mohammad Norouzi, and David J Fleet · 2022
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Equivariant diffusion for molecule generation in 3D
Emiel Hoogeboom, Víctor Garcia Satorras, Clément Vignac, and Max Welling · 2022
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Learning inverse folding from millions of predicted structures
Chloe Hsu, Robert Verkuil, Jason Liu, Zeming Lin, Brian Hie, Tom Sercu, Adam Lerer, and Alexander Rives · 2022
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A backbone-centred energy function of neural networks for protein design
Bin Huang, Yang Xu, Xiuhong Hu, Yongrui Liu, Shanhui Liao, Jiahai Zhang, Chengdong Huang, Jingjun Hong, Quan Chen, and Haiyan Liu · 2022
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ProteinSGM: Score-based generative modeling for de novo protein design
Jin Sub Lee and Philip M Kim · 2022
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Antigen-specific antibody design and optimization with diffusion-based generative models
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, and Jianzhu Ma · 2022
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A deep SE(3)-equivariant model for learning inverse protein folding
Matt McPartlon, Ben Lai, and Jinbo Xu · 2022
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Palette: Image-to-image diffusion models
Chitwan Saharia, William Chan, Huiwen Chang, Chris Lee, Jonathan Ho, Tim Salimans, David Fleet, and Mohammad Norouzi · 2022
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Scaffolding protein functional sites using deep learning
Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Joseph L. Watson, Karla M. Castro, Robert Ragotte, Amijai Saragovi, Lukas F. Milles, Minkyung Baek, Ivan Anishchenko, Wei Yang, Derrick R. Hicks, Marc Expòsit, Thomas Schlichthaerle, Jung-Ho Chun, Justas Dauparas, Nathaniel Bennett, Basile I. M. Wicky, Andrew Muenks, Frank DiMaio, Bruno Correia, Sergey Ovchinnikov, and David Baker · 2022
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GeoDiff: A Geometric Diffusion Model for Molecular Conformation Generation
Minkai Xu, Lantao Yu, Yang Song, Chence Shi, Stefano Ermon, and Jian Tang · 2022
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