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Enzyme design is a critical area in biotechnology, with applications ranging from drug development to synthetic biology.
Molecules as documents of evolutionary history
Emile Zuckerkandl and Linus Pauling · 1965
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Enzyme recruitment in evolution of new function
Roy A Jensen · 1976
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Determining the chemical mechanisms of enzyme-catalyzed reactions by kinetic studies
W Wallace Cleland · 1977
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How do enzymes work?
Joseph Kraut · 1988
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Basic local alignment search tool
Stephen F Altschul, Warren Gish, Webb Miller, Eugene W Myers, and David J Lipman · 1990
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Artificial enzymes
Yukito Murakami, Jun-ichi Kikuchi, Yoshio Hisaeda, and Osamu Hayashida · 1996
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Gapped blast and psi-blast: a new generation of protein database search programs
Stephen F Altschul, Thomas L Madden, Alejandro A Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J Lipman · 1997
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Protein folds and functions
Andrew CR Martin, Christine A Orengo, E Gail Hutchinson, Susan Jones, Maria Karmirantzou, Roman A Laskowski, John BO Mitchell, Chiara Taroni, and Janet M Thornton · 1998
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Protein folds, functions and evolution
Janet M Thornton, Christine A Orengo, Annabel E Todd, and Frances MG Pearl · 1999
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The enzyme database in 2000
Amos Bairoch · 2000
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Enzyme function less conserved than anticipated
Burkhard Rost · 2002
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Brenda: a resource for enzyme data and metabolic information
Ida Schomburg, Antje Chang, Oliver Hofmann, Christian Ebeling, Frank Ehrentreich, and Dietmar Schomburg · 2002
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The gene ontology (go) database and informatics resource
Gene Ontology Consortium · 2004
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The pdbbind database: Collection of binding affinities for protein- ligand complexes with known three-dimensional structures
Renxiao Wang, Xueliang Fang, Yipin Lu, and Shaomeng Wang · 2004
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Simulating protein evolution in sequence and structure space
Yu Xia and Michael Levitt · 2004
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Missense meanderings in sequence space: a biophysical view of protein evolution
Mark A DePristo, Daniel M Weinreich, and Daniel L Hartl · 2005
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Automated genome annotation and pathway identification using the kegg orthology (ko) as a controlled vocabulary
Xizeng Mao, Tao Cai, John G Olyarchuk, and Liping Wei · 2005
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Evolution of enzyme superfamilies
Margaret E Glasner, John A Gerlt, and Patricia C Babbitt · 2006
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An integrated view of protein evolution
Csaba Pál, Balázs Papp, and Martin J Lercher · 2006
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Activity-based protein profiling for the functional annotation of enzymes
Katherine T Barglow and Benjamin F Cravatt · 2007
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Cofactor regeneration for sustainable enzymatic biosynthesis
Wenfang Liu and Ping Wang · 2007
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Assessing the evolutionary impact of amino acid mutations in the human genome
Adam R Boyko, Scott H Williamson, Amit R Indap, Jeremiah D Degenhardt, Ryan D Hernandez, Kirk E Lohmueller, Mark D Adams, Steffen Schmidt, John J Sninsky, Shamil R Sunyaev, et al · 2008
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Structure and function of enzymes involved in the biosynthesis of phenylpropanoids
J-L Ferrer, MB Austin, C Stewart Jr, and JP Noel · 2008
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Protein design by directed evolution
Christian Jäckel, Peter Kast, and Donald Hilvert · 2008
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In the light of directed evolution: pathways of adaptive protein evolution
Jesse D Bloom and Frances H Arnold · 2009
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Manufacturing molecules through metabolic engineering
Jay D Keasling · 2010
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Autodock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Oleg Trott and Arthur J Olson · 2010
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Open babel: An open chemical toolbox
Noel M O’Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, and Geoffrey R Hutchison · 2011
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Cell-free synthetic biology: thinking outside the cell
C Eric Hodgman and Michael C Jewett · 2012
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Proteins: structure and function
David Whitford · 2013
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Protein folding and de novo protein design for biotechnological applications
George A Khoury, James Smadbeck, Chris A Kieslich, and Christodoulos A Floudas · 2014
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Biophysics of protein evolution and evolutionary protein biophysics
Tobias Sikosek and Hue Sun Chan · 2014
Cited alongside, same era.
Structure-based design of inhibitors of protein–protein interactions: mimicking peptide binding epitopes
Marta Pelay-Gimeno, Adrian Glas, Oliver Koch, and Tom N Grossmann · 2015
Cited alongside, same era.
The role of protein dynamics in the evolution of new enzyme function
Eleanor Campbell, Miriam Kaltenbach, Galen J Correy, Paul D Carr, Benjamin T Porebski, Emma K Livingstone, Livnat Afriat-Jurnou, Ashley M Buckle, Martin Weik, Florian Hollfelder, et al · 2016
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Applications of microbial cytochrome p450 enzymes in biotechnology and synthetic biology
Hazel M Girvan and Andrew W Munro · 2016
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Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Martin Steinegger and Johannes Söding · 2017
Cited alongside, same era.
Flow straight and fast: Learning to generate and transfer data with rectified flow, 2022
Xingchao Liu, Chengyue Gong, and Qiang Liu · 2022
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Revisiting heterophily for graph neural networks
Sitao Luan, Chenqing Hua, Qincheng Lu, Jiaqi Zhu, Mingde Zhao, Shuyuan Zhang, Xiao-Wen Chang, and Doina Precup · 2022
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Exploiting enzyme evolution for computational protein design
Gaspar P Pinto, Marina Corbella, Andrey O Demkiv, and Shina Caroline Lynn Kamerlin · 2022
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Scannet: an interpretable geometric deep learning model for structure-based protein binding site prediction
Jérôme Tubiana, Dina Schneidman-Duhovny, and Haim J Wolfson · 2022
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Foldseek: fast and accurate protein structure search
Michel van Kempen, Stephanie S Kim, Charlotte Tumescheit, Milot Mirdita, Cameron LM Gilchrist, Johannes Söding, and Martin Steinegger · 2022
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Metabolite–enzyme coevolution: from single enzymes to metabolic pathways and networks
Lianet Noda-Garcia, Wolfram Liebermeister, and Dan S Tawfik · 2018
Cited alongside, same era.
Homology-based hydrogen bond information improves crystallographic structures in the pdb
Bart van Beusekom, Wouter G Touw, Mahidhar Tatineni, Sandeep Somani, Gunaretnam Rajagopal, Jinquan Luo, Gary L Gilliland, Anastassis Perrakis, and Robbie P Joosten · 2018
Cited alongside, same era.
End-to-end differentiable learning of protein structure
Mohammed AlQuraishi · 2019
Cited alongside, same era.
eggnog 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, et al · 2019
Cited alongside, same era.
Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers
Jae Yong Ryu, Hyun Uk Kim, and Sang Yup Lee · 2019
Cited alongside, same era.
Pushing the boundaries of molecular representation for drug discovery with the graph attention mechanism
Zhaoping Xiong, Dingyan Wang, Xiaohong Liu, Feisheng Zhong, Xiaozhe Wan, Xutong Li, Zhaojun Li, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, et al · 2019
Cited alongside, same era.
Machine-learning-guided directed evolution for protein engineering
Kevin K Yang, Zachary Wu, and Frances H Arnold · 2019
Cited alongside, same era.
Protein representation learning by geometric structure pretraining
Zuobai Zhang, Minghao Xu, Arian Jamasb, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, and Jian Tang · 2022
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Building normalizing flows with stochastic interpolants, 2023
Michael S. Albergo and Eric Vanden-Eijnden · 2023
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Se (3)-stochastic flow matching for protein backbone generation
Avishek Joey Bose, Tara Akhound-Sadegh, Kilian Fatras, Guillaume Huguet, Jarrid Rector-Brooks, Cheng-Hao Liu, Andrei Cristian Nica, Maksym Korablyov, Michael Bronstein, and Alexander Tong · 2023
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Enzymes: a practical introduction to structure, mechanism, and data analysis
Robert A Copeland · 2023
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Atomic context-conditioned protein sequence design using ligandmpnn
Justas Dauparas, Gyu Rie Lee, Robert Pecoraro, Linna An, Ivan Anishchenko, Cameron Glasscock, and David Baker · 2023
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Enzymemap: curation, validation and data-driven prediction of enzymatic reactions
Esther Heid, Daniel Probst, William H Green, and Georg KH Madsen · 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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Mudiff: Unified diffusion for complete molecule generation
Chenqing Hua, Sitao Luan, Minkai Xu, Rex Ying, Jie Fu, Stefano Ermon, and Doina Precup · 2023
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Structure-based drug design with geometric deep learning
Clemens Isert, Kenneth Atz, and Gisbert Schneider · 2023
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Harmonic self-conditioned flow matching for multi-ligand docking and binding site design
Hannes Stärk, Bowen Jing, Regina Barzilay, and Tommi Jaakkola · 2023
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De novo design of protein structure and function with rfdiffusion
Joseph L Watson, David Juergens, Nathaniel R Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach, Woody Ahern, Andrew J Borst, Robert J Ragotte, Lukas F Milles, et al · 2023
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Enzyme function prediction using contrastive learning
Tianhao Yu, Haiyang Cui, Jianan Canal Li, Yunan Luo, Guangde Jiang, and Huimin Zhao · 2023
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Accurate structure prediction of biomolecular interactions with alphafold 3
Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J Ballard, Joshua Bambrick, et al · 2024
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Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, and Tommi Jaakkola · 2024
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Chai-1 technical report
Chai · 2024
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An all-atom protein generative model
Alexander E Chu, Jinho Kim, Lucy Cheng, Gina El Nesr, Minkai Xu, Richard W Shuai, and Po-Ssu Huang · 2024
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Limitations of current machine-learning models in predicting enzymatic functions for uncharacterized proteins
Valerie de Crecy-Lagard, Raquel Dias, Iddo Friedberg, Yifeng Yuan, and Manal Swairjo · 2024
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Simulating 500 million years of evolution with a language model
Tomas Hayes, Roshan Rao, Halil Akin, Nicholas J Sofroniew, Deniz Oktay, Zeming Lin, Robert Verkuil, Vincent Q Tran, Jonathan Deaton, Marius Wiggert, et al · 2024
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Generalized biomolecular modeling and design with rosettafold all-atom
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Yeqing Lin, Minji Lee, Zhao Zhang, and Mohammed AlQuraishi · 2024
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Dynamicbind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
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Clipzyme: Reaction-conditioned virtual screening of enzymes
Peter G Mikhael, Itamar Chinn, and Regina Barzilay · 2024
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Care: a benchmark suite for the classification and retrieval of enzymes
Jason Yang, Ariane Mora, Shengchao Liu, Bruce J Wittmann, Anima Anandkumar, Frances H Arnold, and Yisong Yue · 2024
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Ecloudgen: Access to broader chemical space for structure-based molecule generation
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