Computational design of a cutinase for plastic biodegradation by mining molecular dynamics simulations trajectories

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

(2021) Yinglu Cui et al.   ACS Catalysis

An extracellular lipase from Amycolatopsis mediterannei is a cutinase with plastic degrading activity

(2021) Yeqi Tan et al.   Computational and Structural Biotechnology Journal

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

(2021) Kun Chen et al.   ACS Catalysis

Fluorescence-activated droplet sorting of PET degrading microorganisms

(2021) Yuxin Qiao et al.   JOURNAL OF HAZARDOUS MATERIALS

Improving the accuracy of protein thermostability predictions for single point mutations - Effects of unfolded states and methods for proline mutations

(2020) Jianxin Duan et al.   BIOPHYSICAL JOURNAL

An engineered PET depolymerase to break down and recycle plastic bottles

(2020) V. Tournier et al.   NATURE

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years

(2020) Rahul Nikam et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Hyeoncheol Francis Son et al.   ACS Catalysis

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

(2019) Huali Cao et al.   Journal of Chemical Information and Modeling

Structural and dynamical thermostability of psychrophilic enzyme at various temperatures: Molecular dynamics simulations of tryptophan synthase

(2019) Tamsila Parveen et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Secondary Forces in Protein Folding

(2019) Robert W. Newberry et al.   ACS Chemical Biology

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Oxidative Stress and Advanced Lipoxidation and Glycation End Products (ALEs and AGEs) in Aging and Age-Related Diseases

(2019) Nurbubu T. Moldogazieva et al.   Oxidative Medicine and Cellular Longevity

Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations

(2019) Qingbin Li et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Machine Learning for Prioritization of Thermostabilizing Mutations for G-Protein Coupled Receptors

(2019) Sanychen Muk et al.   BIOPHYSICAL JOURNAL

The hybrid protein interactome contributes to rice heterosis as epistatic effects

(2019) Hong Li et al.   PLANT JOURNAL

Hydrogen Bonds: Simple after All?

(2018) Daniel Herschlag et al.   BIOCHEMISTRY

Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles

(2018) Matthew Carter Childers et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2018) Seongjoon Joo et al.   Nature Communications

Molecular dynamics simulation of potentiometric sensor response: the effect of biomolecules, surface morphology and surface charge

(2018) B. M. Lowe et al.   Nanoscale

CHARMM force field for protonated polyethyleneimine

(2018) Titus Adrian Beu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Screening of commercial enzymes for poly(ethylene terephthalate) (PET) hydrolysis and synergy studies on different substrate sources

(2017) Aline Machado de Castro et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

(2017) Ren Wei et al.   Microbial Biotechnology

Recycling of poly(ethylene terephthalate) – A review focusing on chemical methods

(2016) B. Geyer et al.   Express Polymer Letters

Thermostability of Enzymes from Molecular Dynamics Simulations

(2016) Tim Zeiske et al.   Journal of Chemical Theory and Computation

Integrative analysis of human omics data using biomolecular networks

(2016) Jonathan L. Robinson et al.   Molecular BioSystems

A disulfide bridge in the calcium binding site of a polyester hydrolase increases its thermal stability and activity against polyethylene terephthalate

(2016) Johannes Then et al.   FEBS Open Bio

Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein

(2016) Serena Leone et al.   PLoS One

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

Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality

(2015) Amanda Tse et al.   Journal of Chemical Information and Modeling

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

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

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

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

Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site

(2014) Yuan Xie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Surface engineering of a cutinase fromThermobifida cellulosilyticafor improved polyester hydrolysis

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

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

A graphical interface for the FoldX forcefield

(2011) J. Van Durme et al.   BIOINFORMATICS

Engineered Thermobifida fusca cutinase with increased activity on polyester substrates

(2011) Carla Silva et al.   Biotechnology Journal

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease

(2010) Neema L. Salimi et al.   PLoS Computational Biology

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols