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Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology.
“Quantitation of protein”
C Stoscheck · 1990
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“Quantitation of protein”
C Stoscheck · 1990
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“VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 å resolution and mutational analysis of the interface”
Yves Muller et al · 1998
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“VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 å resolution and mutational analysis of the interface”
Yves Muller et al · 1998
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“DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis”
David Hoover and Jacek Lubkowski · 2002
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“DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis”
David Hoover and Jacek Lubkowski · 2002
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“Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy”
Peter Rosenthal and Richard Henderson · 2003
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“Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy”
Peter Rosenthal and Richard Henderson · 2003
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“Coot: model-building tools for molecular graphics”
Paul Emsley and Kevin Cowtan · 2004
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“Coot: model-building tools for molecular graphics”
Paul Emsley and Kevin Cowtan · 2004
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“Selecting and screening recombinant antibody libraries”
Hennie Hoogenboom · 2005
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“Novel potent orally active selective VEGFR-2 tyrosine kinase inhibitors:synthesis, structure-activity relationships, and antitumor activitiesof N-phenyl-N’-{4-(4-quinolyloxy)phenyl}ureas”
Kazuo Kubo et al · 2005
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“Selecting and screening recombinant antibody libraries”
Hennie Hoogenboom · 2005
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“Novel potent orally active selective VEGFR-2 tyrosine kinase inhibitors:synthesis, structure-activity relationships, and antitumor activitiesof N-phenyl-N’-{4-(4-quinolyloxy)phenyl}ureas”
Kazuo Kubo et al · 2005
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“Bevacizumab, a humanized anti-angiogenic monoclonal antibody for the treatment of colorectal cancer”
I Krämer and H-P Lipp · 2007
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“High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method”
R Gietz and Robert Schiestl · 2007
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“ Phaser
Airlie McCoy et al · 2007
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“Bevacizumab, a humanized anti-angiogenic monoclonal antibody for the treatment of colorectal cancer”
I Krämer and H-P Lipp · 2007
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“High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method”
R Gietz and Robert Schiestl · 2007
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“ Phaser
Airlie McCoy et al · 2007
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“Protein–protein interaction and quaternary structure”
Joël Janin, Ranjit Bahadur and Pinak Chakrabarti · 2008
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“Therapeutic Anti-VEGF Antibodies”
S Lien and H Lowman · 2008
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“Protein–protein interaction and quaternary structure”
Joël Janin, Ranjit Bahadur and Pinak Chakrabarti · 2008
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“Therapeutic Anti-VEGF Antibodies”
S Lien and H Lowman · 2008
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“Solution of the structure of the TNF-TNFR2 complex”
Yohei Mukai et al · 2010
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“Features and development of coot
P Emsley, B Lohkamp, W Scott and K Cowtan · 2010
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“Hidden Markov model speed heuristic and iterative HMM search procedure”
L Johnson, Sean Eddy and Elon Portugaly · 2010
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“Solution of the structure of the TNF-TNFR2 complex”
Yohei Mukai et al · 2010
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“Features and development of coot
P Emsley, B Lohkamp, W Scott and K Cowtan · 2010
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“Hidden Markov model speed heuristic and iterative HMM search procedure”
L Johnson, Sean Eddy and Elon Portugaly · 2010
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“Computational design of proteins targeting the conserved stem region of influenza hemagglutinin”
Sarel Fleishman et al · 2011
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“ REFMAC
Garib Murshudov et al · 2011
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“Computational design of proteins targeting the conserved stem region of influenza hemagglutinin”
Sarel Fleishman et al · 2011
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“ REFMAC
Garib Murshudov et al · 2011
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“Prevention of overfitting in cryo-EM structure determination”
Sjors Scheres and Shaoxia Chen · 2012
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“Prevention of overfitting in cryo-EM structure determination”
Sjors Scheres and Shaoxia Chen · 2012
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“Comparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view”
Shi Hu et al · 2013
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“Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor”
Camille Daniel et al · 2013
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“Comparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view”
Shi Hu et al · 2013
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“Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor”
Camille Daniel et al · 2013
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“Measuring affinity constants of 1450 monoclonal antibodies to peptide targets with a microarray-based label-free assay platform”
J Landry, Yaohuang Ke, Guo-Liang Yu and X Zhu · 2014
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“A computationally designed inhibitor of an Epstein-Barr viral bcl-2 protein induces apoptosis in infected cells”
Erik Procko et al · 2014
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“A computationally designed inhibitor of an Epstein-Barr viral bcl-2 protein induces apoptosis in infected cells”
Erik Procko et al · 2014
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“Measuring affinity constants of 1450 monoclonal antibodies to peptide targets with a microarray-based label-free assay platform”
J Landry, Yaohuang Ke, Guo-Liang Yu and X Zhu · 2014
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“A computationally designed inhibitor of an Epstein-Barr viral bcl-2 protein induces apoptosis in infected cells”
Erik Procko et al · 2014
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“A computationally designed inhibitor of an Epstein-Barr viral bcl-2 protein induces apoptosis in infected cells”
Erik Procko et al · 2014
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“Gctf: Real-time CTF determination and correction”
Kai Zhang · 2015
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“Gctf: Real-time CTF determination and correction”
Kai Zhang · 2015
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“MolProbity: More and better reference data for improved all-atom structure validation”
Christopher Williams et al · 2018
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“MolProbity: More and better reference data for improved all-atom structure validation”
Christopher Williams et al · 2018
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“Effect of bevacizumab on the tight junction proteins of vascular endothelial cells”
Yanan Jia et al · 2019
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“De novo design of potent and selective mimics of IL-2 and IL-15”
Daniel-Adriano Silva et al · 2019
Cited alongside, same era.
“Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs”
Tristan Bepler et al · 2019
Cited alongside, same era.
“Effect of bevacizumab on the tight junction proteins of vascular endothelial cells”
Yanan Jia et al · 2019
Cited alongside, same era.
“De novo design of potent and selective mimics of IL-2 and IL-15”
Daniel-Adriano Silva et al · 2019
Cited alongside, same era.
“Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs”
Tristan Bepler et al · 2019
Cited alongside, same era.
“De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”
Longxing Cao et al · 2020
“Illuminating protein space with a programmable generative model”
John Ingraham et al · 2023
Later among the works it cites.
“Evolutionary-scale prediction of atomic-level protein structure with a language model”
Zeming Lin et al · 2023
Later among the works it cites.
“The dawn of a New Era: Targeting the “undruggables” with antibody-based therapeutics”
Linghui Qian et al · 2023
Later among the works it cites.
“De novo design of protein structure and function with RFdiffusion”
Joseph Watson et al · 2023
Later among the works it cites.
“The CCP
Jon Agirre et al · 2023
Later among the works it cites.
“Improving de novo protein binder design with deep learning”
Nathaniel Bennett et al · 2023
Later among the works it cites.
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Cited alongside, same era.
“Engineered protein scaffolds as next-generation therapeutics”
Michaela Gebauer and Arne Skerra · 2020
Cited alongside, same era.
“Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein”
Alexandra Walls et al · 2020
Cited alongside, same era.
“De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”
Longxing Cao et al · 2020
Cited alongside, same era.
“How to measure and evaluate binding affinities”
Inga Jarmoskaite, Ishraq AlSadhan, Pavanapuresan Vaidyanathan and Daniel Herschlag · 2020
Cited alongside, same era.
“SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects”
Antoni Wrobel et al · 2020
Cited alongside, same era.
“De novo design of picomolar SARS-CoV-2 miniprotein inhibitors”
Longxing Cao et al · 2020
Cited alongside, same era.
“Improvement of cryo-EM maps by simultaneous local and non-local deep learning”
Jiahua He, Tao Li and Sheng-You Huang · 2023
Later among the works it cites.
“De novo design of protein structure and function with RFdiffusion”
Joseph Watson et al · 2023
Later among the works it cites.
“De novo design of protein interactions with learned surface fingerprints”
Pablo Gainza et al · 2023
Later among the works it cites.
“In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models”
Odessa Goudy et al · 2023
Later among the works it cites.
“Illuminating protein space with a programmable generative model”
John Ingraham et al · 2023
Later among the works it cites.
“Evolutionary-scale prediction of atomic-level protein structure with a language model”
Zeming Lin et al · 2023
Later among the works it cites.
“The dawn of a New Era: Targeting the “undruggables” with antibody-based therapeutics”
Linghui Qian et al · 2023
Later among the works it cites.
“De novo design of protein structure and function with RFdiffusion”
Joseph Watson et al · 2023
Later among the works it cites.
“The CCP
Jon Agirre et al · 2023
Later among the works it cites.
“Improving de novo protein binder design with deep learning”
Nathaniel Bennett et al · 2023
Later among the works it cites.
“Improvement of cryo-EM maps by simultaneous local and non-local deep learning”
Jiahua He, Tao Li and Sheng-You Huang · 2023
Later among the works it cites.
“De novo design of protein structure and function with RFdiffusion”
Joseph Watson et al · 2023
Later among the works it cites.
“Accurate structure prediction of biomolecular interactions with AlphaFold 3”
Josh Abramson et al · 2024
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“Preclinical proof of principle for orally delivered Th17 antagonist miniproteins”
Stephanie Berger et al · 2024
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“Sparks of function by de novo protein design”
Alexander Chu, Tianyu Lu and Po-Ssu Huang · 2024
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“Simulating 500 million years of evolution with a language model”
Thomas Hayes et al · 2024
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“AlphaFold two years on: Validation and impact”
Oleg Kovalevskiy, Juan Mateos-Garcia and Kathryn Tunyasuvunakool · 2024
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“Generalized biomolecular modeling and design with RoseTTAFold All-Atom”
Rohith Krishna et al · 2024
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“Machine learning for functional protein design”
Pascal Notin et al · 2024
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“Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences”, 2024
Jeffrey Ruffolo et al · 2024
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“Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign”
Marianne Shawe-Taylor et al · 2024
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“Structure and function of therapeutic antibodies approved by the US FDA in 2023”
William Strohl · 2024
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“De novo design of high-affinity binders of bioactive helical peptides”
Susana Vázquez et al · 2024
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“Sequence-specific targeting of intrinsically disordered protein regions”
Kejia Wu et al · 2024
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“Design of high affinity binders to convex protein target sites”
Wei Yang et al · 2024
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“Accurate structure prediction of biomolecular interactions with AlphaFold 3”
Josh Abramson et al · 2024
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“Data-driven regularization lowers the size barrier of cryo-EM structure determination”
Dari Kimanius et al · 2024
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“Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign”
Marianne Shawe-Taylor et al · 2024
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“Accurate structure prediction of biomolecular interactions with AlphaFold 3”
Josh Abramson et al · 2024
Closest in time.
“Preclinical proof of principle for orally delivered Th17 antagonist miniproteins”
Stephanie Berger et al · 2024
Closest in time.
“Sparks of function by de novo protein design”
Alexander Chu, Tianyu Lu and Po-Ssu Huang · 2024
Closest in time.
“Simulating 500 million years of evolution with a language model”
Thomas Hayes et al · 2024
Closest in time.
“AlphaFold two years on: Validation and impact”
Oleg Kovalevskiy, Juan Mateos-Garcia and Kathryn Tunyasuvunakool · 2024
Closest in time.
“Generalized biomolecular modeling and design with RoseTTAFold All-Atom”
Rohith Krishna et al · 2024
Closest in time.
“Machine learning for functional protein design”
Pascal Notin et al · 2024
Closest in time.
“Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences”, 2024
Jeffrey Ruffolo et al · 2024
Closest in time.
“Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign”
Marianne Shawe-Taylor et al · 2024
Closest in time.
“Structure and function of therapeutic antibodies approved by the US FDA in 2023”
William Strohl · 2024
Closest in time.
“De novo design of high-affinity binders of bioactive helical peptides”
Susana Vázquez et al · 2024
Closest in time.
“Sequence-specific targeting of intrinsically disordered protein regions”
Kejia Wu et al · 2024
Closest in time.
“Design of high affinity binders to convex protein target sites”
Wei Yang et al · 2024
Closest in time.
“Accurate structure prediction of biomolecular interactions with AlphaFold 3”
Josh Abramson et al · 2024
Closest in time.
“Data-driven regularization lowers the size barrier of cryo-EM structure determination”
Dari Kimanius et al · 2024
Closest in time.
“Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign”
Marianne Shawe-Taylor et al · 2024
Closest in time.