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Proteins are macromolecules responsible for essential functions in almost all living organisms.
Interrelationship between structure and function in hemoglobin and myoglobin
Eraldo Antonini · 1965
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Mechanisms of ligand recognition in myoglobin
Barry A Springer, Stephen G Sligar, John S Olson, and George N Jr Phillips · 1994
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Design by directed evolution
Frances H Arnold · 1998
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An introduction to mcmc for machine learning
Christophe Andrieu, Nando De Freitas, Arnaud Doucet, and Michael I Jordan · 2003
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Design and evolution of new catalytic activity with an existing protein scaffold
Hee-Sung Park, Sung-Hun Nam, Jin Kak Lee, Chang No Yoon, Bengt Mannervik, Stephen J Benkovic, and Hak-Sung Kim · 2006
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Metallo beta lactamases in pseudomonas aeruginosa and acinetobacter species
Varsha Gupta · 2008
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Assessment of therapeutic efficacy and fate of engineered human mesenchymal stem cells for cancer therapy
Laura S Sasportas, Randa Kasmieh, Hiroaki Wakimoto, Shawn Hingtgen, Jeroen AJM van de Water, Gayatry Mohapatra, Jose Luiz Figueiredo, Robert L Martuza, Ralph Weissleder, and Khalid Shah · 2009
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Suitemsa: visual tools for multiple sequence alignment comparison and molecular sequence simulation
Catherine L Anderson, Cory L Strope, and Etsuko N Moriyama · 2011
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Strategy and success for the directed evolution of enzymes
Paul A Dalby · 2011
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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, et al · 2011
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De novo enzyme design using rosetta3
Florian Richter, Andrew Leaver-Fay, Sagar D Khare, Sinisa Bjelic, and David Baker · 2011
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Metallo- β \beta -lactamase structure and function
Timothy Palzkill · 2013
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Methods for the directed evolution of proteins
Michael S Packer and David R Liu · 2015
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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
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Directed evolution: bringing new chemistry to life
Frances H Arnold · 2018
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David H Brookes and Jennifer Listgarten · 2018
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Model-based reinforcement learning for biological sequence design
Christof Angermueller, David Dohan, David Belanger, Ramya Deshpande, Kevin Murphy, and Lucy Colwell · 2019
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Biological sequences design using batched bayesian optimization
David Belanger, Suhani Vora, Zelda Mariet, Ramya Deshpande, David Dohan, Christof Angermueller, Kevin Murphy, Olivier Chapelle, and Lucy Colwell · 2019
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Conditioning by adaptive sampling for robust design
David Brookes, Hahnbeom Park, and Jennifer Listgarten · 2019
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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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Learning from protein structure with geometric vector perceptrons
Bowen Jing, Stephan Eismann, Patricia Suriana, Raphael JL Townshend, and Ron Dror · 2020
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Model inversion networks for model-based optimization
Aviral Kumar and Sergey Levine · 2020
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Protein design via deep learning
Wenze Ding, Kenta Nakai, and Haipeng Gong · 2022
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Optimizing molecules using efficient queries from property evaluations
Samuel C Hoffman, Vijil Chenthamarakshan, Kahini Wadhawan, Pin-Yu Chen, and Payel Das · 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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Biological sequence design with gflownets
Moksh Jain, Emmanuel Bengio, Alex Hernandez-Garcia, Jarrid Rector-Brooks, Bonaventure FP Dossou, Chanakya Ajit Ekbote, Jie Fu, Tianyu Zhang, Michael Kilgour, Dinghuai Zhang, et al · 2022
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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
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Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar, Namrata Anand, Raphael R Eguchi, Po-Ssu Huang, and Richard Socher · 2020
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Boss: Bayesian optimization over string spaces
Henry Moss, David Leslie, Daniel Beck, Javier Gonzalez, and Paul Rayson · 2020
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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
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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, et al · 2021
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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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Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations
Payel Das, Tom Sercu, Kahini Wadhawan, Inkit Padhi, Sebastian Gehrmann, Flaviu Cipcigan, Vijil Chenthamarakshan, Hendrik Strobelt, Cicero Dos Santos, Pin-Yu Chen, et al · 2021
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Gnina 1.0: molecular docking with deep learning
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A deep se (3)-equivariant model for learning inverse protein folding
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Proximal exploration for model-guided protein sequence design
Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma, and Jian Peng · 2022
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Protein sequence and structure co-design with equivariant translation
Chence Shi, Chuanrui Wang, Jiarui Lu, Bozitao Zhong, and Jian Tang · 2022
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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 S Jaakkola · 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, et al · 2022
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De novo design of protein interactions with learned surface fingerprints
Pablo Gainza, Sarah Wehrle, Alexandra Van Hall-Beauvais, Anthony Marchand, Andreas Scheck, Zander Harteveld, Stephen Buckley, Dongchun Ni, Shuguang Tan, Freyr Sverrisson, et al · 2023
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Alphafill: enriching alphafold models with ligands and cofactors
Maarten L Hekkelman, Ida de Vries, Robbie P Joosten, and Anastassis Perrakis · 2023
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Yeqing Lin and Mohammed AlQuraishi · 2023
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Importance weighted expectation-maximization for protein sequence design
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De novo design of protein structure and function with rfdiffusion
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Se (3) diffusion model with application to protein backbone generation
Jason Yim, Brian L Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, and Tommi Jaakkola · 2023
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