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Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane (TM) regions.
Amino acid substitution matrices from protein blocks
Steven Henikoff and Jorja G Henikoff · 1992
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Analysis of vibrio cholierae toxr function by construction of novel fusion proteins
Karen M Ottemann and John J Mekalanos · 1995
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Toxcat: a measure of transmembrane helix association in a biological membrane
William P Russ and Donald M Engelman · 1999
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The gxxxg motif: a framework for transmembrane helix-helix association
William P Russ and Donald M Engelman · 2000
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Dimerization of the transmembrane domain of integrin α \alpha iib subunit in cell membranes
Renhao Li, Roman Gorelik, Vikas Nanda, Peter B Law, James D Lear, William F DeGrado, and Joel S Bennett · 2004
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Transmembrane proteins in the protein data bank: identification and classification
Gábor E Tusnády, Zsuzsanna Dosztányi, and István Simon · 2004
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A modified, dual reporter toxcat system for monitoring homodimerization of transmembrane segments of proteins
Maciej Lis and Kenneth Blumenthal · 2006
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Computational design of peptides that target transmembrane helices
Hang Yin, Joanna S. Slusky, Bryan W. Berger, Robin S. Walters, Gaston Vilaire, Rustem I. Litvinov, James D. Lear, Gregory A. Caputo, Joel S. Bennett, and William F. DeGrado · 2007
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De novo design of a transmembrane zn2+-transporting four-helix bundle
Nathan H Joh, Tuo Wang, Manasi P Bhate, Rudresh Acharya, Yibing Wu, Michael Grabe, Mei Hong, Gevorg Grigoryan, and William F DeGrado · 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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Memprotmd: automated insertion of membrane protein structures into explicit lipid membranes
Phillip J Stansfeld, Joseph E Goose, Martin Caffrey, Elisabeth P Carpenter, Joanne L Parker, Simon Newstead, and Mark SP Sansom · 2015
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The membrane-and soluble-protein helix-helix interactome: similar geometry via different interactions
Shao-Qing Zhang, Daniel W Kulp, Chaim A Schramm, Marco Mravic, Ilan Samish, and William F DeGrado · 2015
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Screening for transmembrane association in divisome proteins using toxgreen, a high-throughput variant of the toxcat assay
Claire R Armstrong and Alessandro Senes · 2016
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Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane
Assaf Elazar, Jonathan Weinstein, Ido Biran, Yearit Fridman, Eitan Bibi, and Sarel Jacob Fleishman · 2016
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Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability
Marcin Wolny, Matthew Batchelor, Gail J Bartlett, Emily G Baker, Marta Kurzawa, Peter J Knight, Lorna Dougan, Derek N Woolfson, Emanuele Paci, and Michelle Peckham · 2017
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin · 2018
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The memprotmd database: a resource for membrane-embedded protein structures and their lipid interactions
Thomas D Newport, Mark S P Sansom, and Phillip J Stansfeld · 2019
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Denoising diffusion probabilistic models
Jonathan Ho, Ajay Jain, and Pieter Abbeel · 2020
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Allestm: predicting multiple structural features of transmembrane proteins
Peter Hönigschmid, Stephan Breimann, Martina Weigl, and Dmitrij Frishman · 2020
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Non-full-length water-soluble cxcr4qty and ccr5qty chemokine receptors: Implication for overlooked truncated but functional membrane receptors
Rui Qing, Fei Tao, Pranam Chatterjee, Gaojie Yang, Qiuyi Han, Haeyoon Chung, Jun Ni, Bernhard P Suter, Jan Kubicek, Barbara Maertens, et al · 2020
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Structured denoising diffusion models in discrete state-spaces
Jacob Austin, Daniel D Johnson, Jonathan Ho, Daniel Tarlow, and Rianne Van Den Berg · 2021
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Diffusion models beat gans on image synthesis
Prafulla Dhariwal and Alexander Nichol · 2021
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A reparameterized discrete diffusion model for text generation
Lin Zheng, Jianbo Yuan, Lei Yu, and Lingpeng Kong · 2023
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Computational design of soluble and functional membrane protein analogues
Casper A Goverde, Martin Pacesa, Nicolas Goldbach, Lars J Dornfeld, Petra EM Balbi, Sandrine Georgeon, Stéphane Rosset, Srajan Kapoor, Jagrity Choudhury, Justas Dauparas, et al · 2024
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Protein design with guided discrete diffusion
Nate Gruver, Samuel Stanton, Nathan Frey, Tim GJ Rudner, Isidro Hotzel, Julien Lafrance-Vanasse, Arvind Rajpal, Kyunghyun Cho, and Andrew G Wilson · 2024
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Derivative-free guidance in continuous and discrete diffusion models with soft value-based decoding
Xiner Li, Yulai Zhao, Chenyu Wang, Gabriele Scalia, Gokcen Eraslan, Surag Nair, Tommaso Biancalani, Shuiwang Ji, Aviv Regev, Sergey Levine, et al · 2024
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De novo-designed transmembrane proteins bind and regulate a cytokine receptor
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Andrei L. Lomize, Spencer C. Todd, and Irina D. Pogozheva · 2021
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Correlation of membrane protein conformational and functional dynamics
Raghavendar Reddy Sanganna Gari, Joel José Montalvo-Acosta, George R Heath, Yining Jiang, Xiaolong Gao, Crina M Nimigean, Christophe Chipot, and Simon Scheuring · 2021
Cited alongside, same era.
De novo design of transmembrane β \beta barrels
Anastassia A Vorobieva, Paul White, Binyong Liang, Jim E Horne, Asim K Bera, Cameron M Chow, Stacey Gerben, Sinduja Marx, Alex Kang, Alyssa Q Stiving, et al · 2021
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Deeptmhmm predicts alpha and beta transmembrane proteins using deep neural networks
Jeppe Hallgren, Konstantinos D Tsirigos, Mads Damgaard Pedersen, José Juan Almagro Armenteros, Paolo Marcatili, Henrik Nielsen, Anders Krogh, and Ole Winther · 2022
Cited alongside, same era.
Membrane proteins: structure, function and motion
Masoud Jelokhani-Niaraki · 2022
Cited alongside, same era.
Deeploc 2.0: multi-label subcellular localization prediction using protein language models
Vineet Thumuluri, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Henrik Nielsen, and Ole Winther · 2022
Cited alongside, same era.
Digress: Discrete denoising diffusion for graph generation
Clement Vignac, Igor Krawczuk, Antoine Siraudin, Bohan Wang, Volkan Cevher, and Pascal Frossard · 2022
Cited alongside, same era.
Marco Mravic, Li He, Huong T Kratochvil, Hailin Hu, Sarah E Nick, Weiya Bai, Anne Edwards, Hyunil Jo, Yibing Wu, Daniel DiMaio, et al · 2024
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Simple and effective masked diffusion language models
Subham Sekhar Sahoo, Marianne Arriola, Yair Schiff, Aaron Gokaslan, Edgar Marroquin, Justin T Chiu, Alexander Rush, and Volodymyr Kuleshov · 2024
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Simplified and generalized masked diffusion for discrete data
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Diffusion language models are versatile protein learners
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Multi-objective-guided discrete flow matching for controllable biological sequence design
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Unlocking guidance for discrete state-space diffusion and flow models
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Path planning for masked diffusion model sampling
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Steering masked discrete diffusion models via discrete denoising posterior prediction
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Simple guidance mechanisms for discrete diffusion models
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Gumbel-softmax score and flow matching for discrete biological sequence generation
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Sophia Vincoff, Shrey Goel, Kseniia Kholina, Rishab Pulugurta, Pranay Vure, and Pranam Chatterjee · 2025
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Membrane proteins of known 3d structure
White · 2025
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De novo-designed transmembrane domains tune engineered receptor functions
Assaf Elazar, Nicholas J Chandler, Ashleigh S Davey, Jonathan Y Weinstein, Julie V Nguyen, Raphael Trenker, Ryan S Cross, Misty R Jenkins, Melissa J Call, Matthew E Call, and Sarel J Fleishman · 2050
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