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Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nature.
Rank analysis of incomplete block designs: I. The method of paired comparisons
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Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
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Replacing the complementarity-determining regions in a human antibody with those from a mouse
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Diversity in the CDR3 Region of VH Is Sufficient for Most Antibody Specificities
John L Xu and Mark M Davis. 2000 · 2000
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Germinal centers
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Abdesign: A n algorithm for combinatorial backbone design guided by natural conformations and sequences
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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
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RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D Weitzner, Xiaozhen Hu, Yumiko Adachi, William R Schief, and Roland L Dunbrack Jr. 2018 · 2018
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Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces
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Denoising diffusion probabilistic models on so (3) for rotational alignment
Adam Leach, Sebastian M Schmon, Matteo T Degiacomi, and Chris G Willcocks. 2022 · 2022
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Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, and Jianzhu Ma. 2022 · 2022
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Training language models to follow instructions with human feedback
Long Ouyang, Jeffrey Wu, Xu Jiang, Diogo Almeida, Carroll Wainwright, Pamela Mishkin, Chong Zhang, Sandhini Agarwal, Katarina Slama, Alex Gray, John Schulman, Jacob Hilton, Fraser Kelton, Luke Miller, Maddie Simens, Amanda Askell, Peter Welinder, Paul Christiano, Jan Leike, and Ryan Lowe. 2022 · 2022
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Proximal Preference Optimization for Diffusion Models
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Training diffusion models with reinforcement learning
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Antibody complementarity determining region design using high-capacity machine learning
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A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
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Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail
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Learning from Protein Structure with Geometric Vector Perceptrons
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Highly accurate protein structure prediction with AlphaFold
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Roto-translated Local Coordinate Frames For Interacting Dynamical Systems
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Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design
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AbDiffuser: full-atom generation of in-vitro functioning antibodies
Karolis Martinkus, Jan Ludwiczak, WEI-CHING LIANG, Julien Lafrance-Vanasse, Isidro Hotzel, Arvind Rajpal, Yan Wu, Kyunghyun Cho, Richard Bonneau, Vladimir Gligorijevic, and Andreas Loukas. 2023 · 2023
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Direct Preference Optimization: Your Language Model is Secretly a Reward Model
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Diffusion Model Alignment Using Direct Preference Optimization
Bram Wallace, Meihua Dang, Rafael Rafailov, Linqi Zhou, Aaron Lou, Senthil Purushwalkam, Stefano Ermon, Caiming Xiong, Shafiq Joty, and Nikhil Naik. 2023 · 2023
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A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design
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SE(3) diffusion model with application to protein backbone generation
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Structure-informed Language Models Are Protein Designers
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Self-play fine-tuning converts weak language models to strong language models
Zixiang Chen, Yihe Deng, Huizhuo Yuan, Kaixuan Ji, and Quanquan Gu. 2024 · 2024
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