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Directed Evolution: Bringing New Chemistry to Life
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journal
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November 2017 |
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Epistasis in protein evolution: Epistasis in Protein Evolution
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journal
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February 2016 |
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Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
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journal
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October 2022 |
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Why are proteins marginally stable?
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journal
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December 2001 |
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Machine Learning-driven Protein Library Design: A Path Toward Smarter Libraries
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book
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April 2022 |
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Machine Learning for Protein Engineering
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book
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October 2023 |
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Learning epistatic interactions from sequence-activity data to predict enantioselectivity
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journal
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December 2017 |
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Learning the local landscape of protein structures with convolutional neural networks
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journal
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November 2021 |
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The NK model of rugged fitness landscapes and its application to maturation of the immune response
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journal
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November 1989 |
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Protein sequence design with deep generative models
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December 2021 |
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Structure-based protein design with deep learning
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journal
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December 2021 |
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Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design
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journal
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November 2020 |
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Informed training set design enables efficient machine learning-assisted directed protein evolution
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journal
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August 2021 |
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Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins
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journal
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April 2022 |
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In vitro continuous protein evolution empowered by machine learning and automation
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journal
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August 2023 |
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ProGen2: Exploring the boundaries of protein language models
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journal
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November 2023 |
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Generative design of de novo proteins based on secondary-structure constraints using an attention-based diffusion model
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journal
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July 2023 |
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Machine learning to navigate fitness landscapes for protein engineering
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journal
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June 2022 |
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From sequence to function through structure: Deep learning for protein design
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journal
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January 2023 |
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LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries
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journal
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January 2023 |
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A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
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journal
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November 2014 |
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Why High-error-rate Random Mutagenesis Libraries are Enriched in Functional and Improved Proteins
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journal
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July 2005 |
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The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities
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journal
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October 2023 |
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Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability
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journal
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July 2016 |
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Automated Design of Efficient and Functionally Diverse Enzyme Repertoires
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journal
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October 2018 |
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Stability effects of mutations and protein evolvability
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journal
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October 2009 |
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Advances in machine learning for directed evolution
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journal
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August 2021 |
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Epistasis and intramolecular networks in protein evolution
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journal
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August 2021 |
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Adaptive machine learning for protein engineering
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journal
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February 2022 |
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Deep generative modeling for protein design
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journal
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February 2022 |
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Directed Evolution: Methodologies and Applications
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journal
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July 2021 |
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Deep Dive into Machine Learning Models for Protein Engineering
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journal
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April 2020 |
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CLADE 2.0: Evolution-Driven Cluster Learning-Assisted Directed Evolution
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journal
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September 2022 |
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Exposing the Limitations of Molecular Machine Learning with Activity Cliffs
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journal
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December 2022 |
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QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis
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journal
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August 2023 |
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Analyzing Learned Molecular Representations for Property Prediction
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journal
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July 2019 |
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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journal
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May 2017 |
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Designing Chemical Reaction Arrays Using Phactor and ChatGPT
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journal
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August 2023 |
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Designed High-Redox Potential Laccases Exhibit High Functional Diversity
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journal
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October 2022 |
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Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts
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journal
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February 2023 |
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Structure-Based Design of Small Imine Reductase Panels for Target Substrates
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journal
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September 2023 |
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Machine Learning-Guided Protein Engineering
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journal
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October 2023 |
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Catalyst Energy Prediction with CatBERTa: Unveiling Feature Exploration Strategies through Large Language Models
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journal
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November 2023 |
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Diverse Engineered Heme Proteins Enable Stereodivergent Cyclopropanation of Unactivated Alkenes
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journal
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February 2018 |
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Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules
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journal
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January 2018 |
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Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction
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journal
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August 2019 |
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100th Anniversary of Macromolecular Science Viewpoint: Data-Driven Protein Design
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journal
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February 2021 |
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Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning
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journal
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October 2020 |
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evSeq: Cost-Effective Amplicon Sequencing of Every Variant in a Protein Library
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journal
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February 2022 |
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“Multiagent” Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations
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journal
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May 2022 |
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Coherent Blending of Biophysics-Based Knowledge with Bayesian Neural Networks for Robust Protein Property Prediction
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journal
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October 2023 |
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ProtWave-VAE: Integrating Autoregressive Sampling with Latent-Based Inference for Data-Driven Protein Design
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journal
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November 2023 |
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DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering
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journal
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July 2023 |
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Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins
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journal
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August 2018 |
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Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes
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journal
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December 2014 |
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Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
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journal
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May 2006 |
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Repertoire of Computationally Designed Peroxygenases for Enantiodivergent C–H Oxyfunctionalization Reactions
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journal
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January 2023 |
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Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site
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journal
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June 2023 |
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Using Data Science for Mechanistic Insights and Selectivity Predictions in a Non-Natural Biocatalytic Reaction
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journal
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August 2023 |
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Natural Selection and the Concept of a Protein Space
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journal
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February 1970 |
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Engineering the third wave of biocatalysis
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journal
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May 2012 |
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The coming of age of de novo protein design
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journal
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September 2016 |
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Mutation effects predicted from sequence co-variation
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journal
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January 2017 |
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Molecular evolution by staggered extension process (StEP) in vitro recombination
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March 1998 |
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Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway
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journal
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November 2015 |
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Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded
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journal
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June 2017 |
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Methods for the directed evolution of proteins
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journal
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June 2015 |
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Exploring protein fitness landscapes by directed evolution
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journal
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December 2009 |
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Protein building blocks preserved by recombination
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journal
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June 2002 |
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Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics
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journal
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March 2021 |
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Protein design and variant prediction using autoregressive generative models
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journal
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April 2021 |
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Structure-based protein function prediction using graph convolutional networks
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journal
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May 2021 |
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Machine learning differentiates enzymatic and non-enzymatic metals in proteins
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journal
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June 2021 |
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Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions
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journal
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September 2021 |
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Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production
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journal
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October 2021 |
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Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
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journal
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March 2022 |
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ProtGPT2 is a deep unsupervised language model for protein design
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journal
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July 2022 |
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Designed active-site library reveals thousands of functional GFP variants
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journal
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May 2023 |
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Rapid planning and analysis of high-throughput experiment arrays for reaction discovery
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journal
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July 2023 |
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The importance of catalytic promiscuity for enzyme design and evolution
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journal
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November 2019 |
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Highly accurate protein structure prediction with AlphaFold
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journal
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July 2021 |
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Disease variant prediction with deep generative models of evolutionary data
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journal
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October 2021 |
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De novo protein design by deep network hallucination
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journal
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December 2021 |
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Mapping the energetic and allosteric landscapes of protein binding domains
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journal
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April 2022 |
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Machine learning-aided engineering of hydrolases for PET depolymerization
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journal
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April 2022 |
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De novo design of luciferases using deep learning
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journal
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February 2023 |
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Mega-scale experimental analysis of protein folding stability in biology and design
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journal
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July 2023 |
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De novo design of protein structure and function with RFdiffusion
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journal
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July 2023 |
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Clustering predicted structures at the scale of the known protein universe
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journal
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September 2023 |
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Unraveling the functional dark matter through global metagenomics
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journal
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October 2023 |
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Deep diversification of an AAV capsid protein by machine learning
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journal
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February 2021 |
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Learning protein fitness models from evolutionary and assay-labeled data
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journal
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January 2022 |
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Using deep learning to annotate the protein universe
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journal
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February 2022 |
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Single-sequence protein structure prediction using a language model and deep learning
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journal
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October 2022 |
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Large language models generate functional protein sequences across diverse families
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journal
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January 2023 |
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Efficient evolution of human antibodies from general protein language models
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journal
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April 2023 |
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Deep generative models of genetic variation capture the effects of mutations
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journal
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September 2018 |
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Machine-learning-guided directed evolution for protein engineering
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journal
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July 2019 |
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Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics
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journal
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October 2019 |
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Unified rational protein engineering with sequence-based deep representation learning
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journal
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October 2019 |
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CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
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journal
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February 2021 |
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Macromolecular modeling and design in Rosetta: recent methods and frameworks
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journal
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June 2020 |
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Low-N protein engineering with data-efficient deep learning
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journal
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April 2021 |
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Systematic molecular evolution enables robust biomolecule discovery
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journal
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December 2021 |
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EnzymeML: seamless data flow and modeling of enzymatic data
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February 2023 |
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Engineering new catalytic activities in enzymes
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journal
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January 2020 |
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Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
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journal
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June 2022 |
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Machine learning-enabled retrobiosynthesis of molecules
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journal
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February 2023 |
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Expanding functional protein sequence spaces using generative adversarial networks
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journal
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March 2021 |
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Controllable protein design with language models
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journal
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June 2022 |
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State-specific protein–ligand complex structure prediction with a multiscale deep generative model
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journal
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February 2024 |
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Biocatalysis
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journal
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June 2021 |
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Cluster learning-assisted directed evolution
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journal
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December 2021 |
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Persistent spectral theory-guided protein engineering
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journal
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February 2023 |
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Combining chemistry and protein engineering for new-to-nature biocatalysis
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journal
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January 2022 |
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Predicting enzymatic reactions with a molecular transformer
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journal
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January 2021 |
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On the conservative nature of intragenic recombination
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journal
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April 2005 |
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Protein stability promotes evolvability
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journal
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March 2006 |
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Navigating the protein fitness landscape with Gaussian processes
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journal
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December 2012 |
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Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins
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journal
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March 2017 |
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Machine learning-assisted directed protein evolution with combinatorial libraries
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journal
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April 2019 |
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Protein stability engineering insights revealed by domain-wide comprehensive mutagenesis
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journal
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August 2019 |
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
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journal
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April 2021 |
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Protein sequence design by conformational landscape optimization
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journal
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March 2021 |
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Neural networks to learn protein sequence–function relationships from deep mutational scanning data
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journal
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November 2021 |
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On the sparsity of fitness functions and implications for learning
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journal
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December 2021 |
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Enhancing computational enzyme design by a maximum entropy strategy
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journal
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February 2022 |
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Conformal prediction under feedback covariate shift for biomolecular design
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journal
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October 2022 |
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Decoupling of catalysis and transition state analog binding from mutations throughout a phosphatase revealed by high-throughput enzymology
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journal
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July 2023 |
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Enhancing luciferase activity and stability through generative modeling of natural enzyme sequences
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journal
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November 2023 |
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Interpretable Numerical Descriptors of Amino Acid Space
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journal
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May 2009 |
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BioGPT: generative pre-trained transformer for biomedical text generation and mining
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journal
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September 2022 |
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Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments
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December 2022 |
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Nucleotide augmentation for machine learning-guided protein engineering
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December 2022 |
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PROSS 2: a new server for the design of stable and highly expressed protein variants
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journal
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December 2020 |
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Enzyme promiscuity prediction using hierarchy-informed multi-label classification
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journal
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January 2021 |
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ProteinBERT: a universal deep-learning model of protein sequence and function
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journal
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February 2022 |
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Predicting enzymatic function of protein sequences with attention
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October 2023 |
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UniProt: the Universal Protein Knowledgebase in 2023
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November 2022 |
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The FoldX web server: an online force field
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July 2005 |
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Protein Design is NP-hard
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journal
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October 2002 |
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Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks
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preprint
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October 2021 |
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MSA Transformer
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preprint
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August 2021 |
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FLIP: Benchmark tasks in fitness landscape inference for proteins
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journal
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January 2022 |
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Function-guided protein design by deep manifold sampling
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preprint
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December 2021 |
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Learning inverse folding from millions of predicted structures
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preprint
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September 2022 |
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Generative power of a protein language model trained on multiple sequence alignments
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preprint
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November 2022 |
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Convolutions are competitive with transformers for protein sequence pretraining
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preprint
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February 2024 |
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Masked inverse folding with sequence transfer for protein representation learning
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preprint
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March 2023 |
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High-resolution de novo structure prediction from primary sequence
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preprint
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July 2022 |
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Advancing Antibiotic Resistance Classification with Deep Learning Using Protein Sequence and Structure
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preprint
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April 2023 |
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GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
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preprint
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November 2022 |
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Tuned Fitness Landscapes for Benchmarking Model-Guided Protein Design
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journal
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October 2022 |
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Protein design using structure-based residue preferences
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preprint
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June 2023 |
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Codon language embeddings provide strong signals for protein engineering
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preprint
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December 2022 |
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Language models generalize beyond natural proteins
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preprint
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December 2022 |
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A high-level programming language for generative protein design
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preprint
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December 2022 |
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ProT-VAE: Protein Transformer Variational AutoEncoder for Functional Protein Design
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preprint
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January 2023 |
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Meta Learning Improves Robustness and Performance in Machine Learning-Guided Protein Engineering
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preprint
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January 2023 |
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Computational Scoring and Experimental Evaluation of Enzymes Generated by Neural Networks
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preprint
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April 2023 |
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What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds
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preprint
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March 2023 |
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Flattening the curve - How to get better results with small deep-mutational-scanning datasets
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preprint
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October 2023 |
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Sequence VS. Structure: Delving Deep into Data-Driven Protein Function Prediction
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preprint
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April 2023 |
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Benchmarking Uncertainty Quantification for Protein Engineering
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preprint
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April 2023 |
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ATOMDANCE: kernel-based denoising and allosteric resonance analysis for functional and evolutionary comparisons of protein dynamics
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journal
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October 2023 |
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AnnoPRO: an Innovative Strategy for Protein Function Annotation based on Image-like Protein Representation and Multimodal Deep Learning
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journal
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May 2023 |
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Self-driving laboratories to autonomously navigate the protein fitness landscape
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preprint
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May 2023 |
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Assessing the performance of protein regression models
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preprint
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September 2023 |
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FLOP: Tasks for Fitness Landscapes Of Protein wildtypes
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preprint
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June 2023 |
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Fine-tuning Protein Embeddings for Generalizable Annotation Propagation
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journal
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June 2023 |
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xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein
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preprint
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January 2024 |
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Learning Complete Protein Representation by Deep Coupling of Sequence and Structure
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preprint
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July 2023 |
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The simplicity of protein sequence-function relationships
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preprint
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September 2023 |
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Protein generation with evolutionary diffusion: sequence is all you need
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preprint
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September 2023 |
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Minimal epistatic networks from integrated sequence and mutational protein data
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preprint
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September 2023 |
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What makes the effect of protein mutations difficult to predict?
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preprint
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September 2023 |
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Removing bias in sequence models of protein fitness
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preprint
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September 2023 |
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Improving protein expression, stability, and function with ProteinMPNN
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preprint
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October 2023 |
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Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
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preprint
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October 2023 |
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Harnessing Generative AI to Decode Enzyme Catalysis and Evolution for Enhanced Engineering
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preprint
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October 2023 |
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Explainable protein function annotation using local structure embeddings
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journal
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October 2023 |
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Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics
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preprint
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October 2023 |
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TRILL: Orchestrating Modular Deep-Learning Workflows for Democratized, Scalable Protein Analysis and Engineering
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preprint
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November 2023 |
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The genetic architecture of protein stability
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preprint
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October 2023 |
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Neural network extrapolation to distant regions of the protein fitness landscape
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preprint
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November 2023 |
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Contrasting Sequence with Structure: Pre-training Graph Representations with PLMs
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preprint
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December 2023 |
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Fine-tuning protein language models boosts predictions across diverse tasks
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preprint
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December 2023 |
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Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution
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preprint
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December 2023 |
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Leveraging ancestral sequence reconstruction for protein representation learning
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preprint
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December 2023 |
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Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models
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preprint
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December 2023 |
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Evaluating Protein Transfer Learning with TAPE
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preprint
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June 2019 |
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Is Novelty Predictable?
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journal
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December 2023 |
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ProtTrans: Towards Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High Performance Computing
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journal
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January 2021 |
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Optimal trade-off control in machine learning–based library design, with application to adeno-associated virus (AAV) for gene therapy
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journal
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January 2024 |
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Protein Dynamism and Evolvability
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journal
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April 2009 |
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Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
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July 2010 |
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An evolution-based model for designing chorismate mutase enzymes
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July 2020 |
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Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics
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July 2021 |
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Accurate prediction of protein structures and interactions using a three-track neural network
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July 2021 |
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Scaffolding protein functional sites using deep learning
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July 2022 |
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Hallucinating symmetric protein assemblies
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journal
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October 2022 |
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Robust deep learning–based protein sequence design using ProteinMPNN
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October 2022 |
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Evolutionary-scale prediction of atomic-level protein structure with a language model
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March 2023 |
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Combinatorial assembly and design of enzymes
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January 2023 |
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Enzyme function prediction using contrastive learning
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March 2023 |
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Accurate proteome-wide missense variant effect prediction with AlphaMissense
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September 2023 |
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A rugged yet easily navigable fitness landscape
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November 2023 |
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From nature to industry: Harnessing enzymes for biocatalysis
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November 2023 |
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Autonomous, multiproperty-driven molecular discovery: From predictions to measurements and back
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December 2023 |
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High-throughput deep learning variant effect prediction with Sequence UNET
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May 2023 |
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How Protein Stability and New Functions Trade Off
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February 2008 |
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Ancestral Reconstruction
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July 2016 |
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Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
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Generating functional protein variants with variational autoencoders
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February 2021 |
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Machine learning modeling of family wide enzyme-substrate specificity screens
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February 2022 |
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Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
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October 2022 |
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Inferring protein fitness landscapes from laboratory evolution experiments
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March 2023 |
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Ancestral protein reconstruction: techniques and applications
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January 2016 |
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Enabling high‐throughput biology with flexible open‐source automation
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Zero-shot prediction of mutation effects on protein function with multimodal deep representation learning
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preprint
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October 2023 |
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EnzymeMap: Curation, validation and data-driven prediction of enzymatic reactions
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preprint
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April 2023 |
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Protein Fitness Prediction Is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods
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April 2023 |
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De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
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Adaptation in protein fitness landscapes is facilitated by indirect paths
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July 2016 |