Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity

Plastics degradation by hydrolytic enzymes: the Plastics‐Active Enzymes Database ‐ PAZy

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The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

(2022) Hongli Zhang et al.   Frontiers in Microbiology

Particle Size Reduction of Poly(ethylene terephthalate) Increases the Rate of Enzymatic Depolymerization But Does Not Increase the Overall Conversion Extent

(2022) Richard K. Brizendine et al.   ACS Sustainable Chemistry & Engineering

Directed evolution of an efficient and thermostable PET depolymerase

(2022) Elizabeth L. Bell et al.   Nature Catalysis

Computational Redesign of a PETase for Plastic Biodegradation under Ambient Condition by the GRAPE Strategy

(2021) Yinglu Cui et al.   ACS Catalysis

Catalytic processing of plastic waste on the rise

(2021) Antonio J. Martín et al.   Chem

Parallel molecular mechanisms for enzyme temperature adaptation

(2021) Margaux M. Pinney et al.   SCIENCE

Generating functional protein variants with variational autoencoders

(2021) Alex Hawkins-Hooker et al.   PLoS Computational Biology

Low-N protein engineering with data-efficient deep learning

(2021) Surojit Biswas et al.   NATURE METHODS

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

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Protein design and variant prediction using autoregressive generative models

(2021) Jung-Eun Shin et al.   Nature Communications

Low Carbon Footprint Recycling of Post‐Consumer PET Plastic with a Metagenomic Polyester Hydrolase

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Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

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Highly accurate protein structure prediction with AlphaFold

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Highly accurate protein structure prediction for the human proteome

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Enzymatic depolymerization of highly crystalline polyethylene terephthalate enabled in moist-solid reaction mixtures

(2021) Sandra Kaabel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Insights into the Enhanced Performance of EKylated PETase Toward PET Degradation

(2021) Kun Chen et al.   ACS Catalysis

Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation

(2021) Akihiko Nakamura et al.   ACS Catalysis

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere

(2021) Robyn J. Wright et al.   Microbiome

Chemical and biological catalysis for plastics recycling and upcycling

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Techno-economic, life-cycle, and socioeconomic impact analysis of enzymatic recycling of poly(ethylene terephthalate)

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A comprehensive and critical review on key elements to implement enzymatic PET depolymerization for recycling purposes

(2021) Adriano Carniel et al.   BIOTECHNOLOGY ADVANCES

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

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Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

An engineered PET depolymerase to break down and recycle plastic bottles

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Current state and perspectives related to the PET hydrolases available for biorecycling

(2020) Fusako Kawai et al.   ACS Sustainable Chemistry & Engineering

Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning

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The highly crystalline PET found in plastic water bottles does not support the growth of the PETase‐producing bacterium Ideonella sakaiensis

(2020) Noah E. Wallace et al.   Environmental Microbiology Reports

Database resources of the National Center for Biotechnology Information

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Possibilities and limitations of biotechnological plastic degradation and recycling

(2020) Ren Wei et al.   Nature Catalysis

Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation

(2019) Hyeoncheol Francis Son et al.   ACS Catalysis

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Biodegradation of PET: Current Status and Application Aspects

(2019) Ikuo Taniguchi et al.   ACS Catalysis

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

(2019) Gang Li et al.   ACS Synthetic Biology

Biocatalytic Degradation Efficiency of Postconsumer Polyethylene Terephthalate Packaging Determined by Their Polymer Microstructures

(2019) Ren Wei et al.   Advanced Science

Plastics: Microbial Degradation, Environmental and Biotechnological Perspectives

(2019) Dominik Danso et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers

(2019) Jae Yong Ryu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate

(2019) Gottfried J. Palm et al.   Nature Communications

DALI and the persistence of protein shape

(2019) Liisa Holm   PROTEIN SCIENCE

Efficient Degradation of Poly(ethylene terephthalate) with Thermobifida fusca Cutinase Exhibiting Improved Catalytic Activity Generated using Mutagenesis and Additive-based Approaches

(2019) Makoto Furukawa et al.   Scientific Reports

Conformational fitting of a flexible oligomeric substrate does not explain the enzymatic PET degradation

(2019) Ren Wei et al.   Nature Communications

Stabilizing Leaf and Branch Compost Cutinase (LCC) with Glycosylation: Mechanism and Effect on PET Hydrolysis

(2018) Abhijit N. Shirke et al.   BIOCHEMISTRY

Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase

(2018) Tobias Fecker et al.   BIOPHYSICAL JOURNAL

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

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Characterization and engineering of a plastic-degrading aromatic polyesterase

(2018) Harry P. Austin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

(2018) Seongjoon Joo et al.   Nature Communications

New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

(2018) Dominik Danso et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

OUP accepted manuscript

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BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis

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Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes

(2018) Saroj Poudel et al.   Frontiers in Microbiology

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

(2018) Martin K. M. Engqvist   BMC MICROBIOLOGY

The deep, hot biosphere: Twenty-five years of retrospection

(2017) Daniel R. Colman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzymatic recovery of polyester building blocks from polymer blends

(2017) Caroline Gamerith et al.   PROCESS BIOCHEMISTRY

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Structural insight into catalytic mechanism of PET hydrolase

(2017) Xu Han et al.   Nature Communications

Biocatalysis as a green route for recycling the recalcitrant plastic polyethylene terephthalate

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Chemical recycling of waste plastics for new materials production

(2017) AliReza Rahimi et al.   Nature Reviews Chemistry

A bacterium that degrades and assimilates poly(ethylene terephthalate)

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Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

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Hydrolysis of synthetic polyesters byClostridium botulinumesterases

(2015) Veronika Perz et al.   BIOTECHNOLOGY AND BIOENGINEERING

Ca2+and Mg2+binding site engineering increases the degradation of polyethylene terephthalate films by polyester hydrolases fromThermobifida fusca

(2015) Johannes Then et al.   Biotechnology Journal

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Ca2+and Mg2+binding site engineering increases the degradation of polyethylene terephthalate films by polyester hydrolases fromThermobifida fusca

(2015) Johannes Then et al.   Biotechnology Journal

Plastic waste as a novel substrate for industrial biotechnology

(2015) Nick Wierckx et al.   Microbial Biotechnology

Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca

(2014) Christian Roth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Crystal Structure and Thermodynamic and Kinetic Stability of Metagenome-Derived LC-Cutinase

(2014) Sintawee Sulaiman et al.   BIOCHEMISTRY

Surface engineering of a cutinase fromThermobifida cellulosilyticafor improved polyester hydrolysis

(2013) Enrique Herrero Acero et al.   BIOTECHNOLOGY AND BIOENGINEERING

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions

(2012) Nicolas Lenfant et al.   NUCLEIC ACIDS RESEARCH

A New Esterase from Thermobifida halotolerans Hydrolyses Polyethylene Terephthalate (PET) and Polylactic Acid (PLA)

(2012) Doris Ribitsch et al.   Polymers

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach

(2011) Sintawee Sulaiman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of a new cutinase fromThermobifida albafor PET-surface hydrolysis

(2011) Doris Ribitsch et al.   BIOCATALYSIS AND BIOTRANSFORMATION

ISPyB: an information management system for synchrotron macromolecular crystallography

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Engineered Thermobifida fusca cutinase with increased activity on polyester substrates

(2011) Carla Silva et al.   Biotechnology Journal

Hydrolysis of polyethyleneterephthalate by p-nitrobenzylesterase from Bacillus subtilis

(2011) Doris Ribitsch et al.   BIOTECHNOLOGY PROGRESS

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

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Features and development ofCoot

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Diversity of polyester-degrading bacteria in compost and molecular analysis of a thermoactive esterase from Thermobifida alba AHK119

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CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants

(2010) Yunqi Li et al.   BMC BIOINFORMATICS

AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties

(2010) Krishna Kumar Kandaswamy et al.   JOURNAL OF THEORETICAL BIOLOGY

Surface structure and properties of poly-(ethylene terephthalate) hydrolyzed by alkali and cutinase

(2010) Ilaria Donelli et al.   POLYMER DEGRADATION AND STABILITY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Cutinase-Catalyzed Hydrolysis of Poly(ethylene terephthalate)

(2009) Åsa M. Ronkvist et al.   MACROMOLECULES

An expert system to predict protein thermostability using decision tree

(2008) Li-Cheng Wu et al.   EXPERT SYSTEMS WITH APPLICATIONS

Pet Waste Management by Chemical Recycling: A Review

(2008) Vijaykumar Sinha et al.   JOURNAL OF POLYMERS AND THE ENVIRONMENT

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

Predicting Protein Subcellular Location Using Chous Pseudo Amino Acid Composition and Improved Hybrid Approach

(2008) Feng-Min Li et al.   PROTEIN AND PEPTIDE LETTERS