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Computational protein design, i.e.
How significant is a protein structure similarity with tm-score= 0.5?
Jinrui Xu and Yang Zhang · 2010
Earlier work this paper cites.
An introduction to sequence similarity (“homology”) searching
William R Pearson · 2013
Earlier work this paper cites.
Anarci: antigen receptor numbering and receptor classification
James Dunbar and Charlotte M Deane · 2016
Earlier work this paper cites.
Nanobodies and nanobody-based human heavy chain antibodies as antitumor therapeutics
Peter Bannas, Julia Hambach, and Friedrich Koch-Nolte · 2017
Earlier work this paper cites.
Yeast surface display platform for rapid discovery of conformationally selective nanobodies
Conor McMahon, Alexander S Baier, Roberta Pascolutti, Marcin Wegrecki, Sanduo Zheng, Janice X Ong, Sarah C Erlandson, Daniel Hilger, Søren GF Rasmussen, and Aaron M Ring · 2018
Earlier work this paper cites.
Unified rational protein engineering with sequence-based deep representation learning
Ethan C Alley, Grigory Khimulya, Surojit Biswas, Mohammed AlQuraishi, and George M Church · 2019
Earlier work this paper cites.
Generative models for graph-based protein design
John Ingraham, Vikas Garg, Regina Barzilay, and Tommi Jaakkola · 2019
Cited alongside, same era.
Evodesign: Designing protein-protein binding interactions using evolutionary interface profiles in conjunction with an optimized physical energy function
Robin Pearce, Xiaoqiang Huang, Dani Setiawan, and Yang Zhang · 2019
Cited alongside, same era.
Learning from protein structure with geometric vector perceptrons
Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael JL Townshend, and Ron Dror · 2020
Cited alongside, same era.
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.
In silico proof of principle of machine learning-based antibody design at unconstrained scale
Rahmad Akbar, Philippe A Robert, Cédric R Weber, Michael Widrich, Robert Frank, Milena Pavlović, Lonneke Scheffer, Maria Chernigovskaya, Igor Snapkov, and Andrei Slabodkin · 2021
Fold2seq: A joint sequence (1d)-fold (3d) embedding-based generative model for protein design
Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, and Yang Shen · 2021
Closest in time.
Indi-integrated nanobody database for immunoinformatics
Piotr Deszynski, Jakub Mlokosiewicz, Adam Volanakis, Igor Jaszczyszyn, Natalie Castellana, Stefano Bonissone, Rajkumar Ganesan, and Konrad Krawczyk · 2021
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Iterative refinement graph neural network for antibody sequence-structure co-design, 2021
Wengong Jin, Jeremy Wohlwend, Regina Barzilay, and Tommi Jaakkola · 2021
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Antibody design using lstm based deep generative model from phage display library for affinity maturation
Koichiro Saka, Taro Kakuzaki, Shoichi Metsugi, Daiki Kashiwagi, Kenji Yoshida, Manabu Wada, Hiroyuki Tsunoda, and Reiji Teramoto · 2021
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Protein design and variant prediction using autoregressive generative models
Jung-Eun Shin, Adam J Riesselman, Aaron W Kollasch, Conor McMahon, Elana Simon, Chris Sander, Aashish Manglik, Andrew C Kruse, and Debora S Marks · 2021
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Cited alongside, same era.