In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO)

Multilayer Engineering of Enzyme Cascade Catalysis for One-Pot Preparation of Nylon Monomers from Renewable Fatty Acids

(2020) Tae-Hun Kim et al.   ACS Catalysis

A Growth-Based, High-Throughput Selection Platform Enables Remodeling of 4-Hydroxybenzoate Hydroxylase Active Site

(2020) Sarah Maxel et al.   ACS Catalysis

In Vivo Selection for Formate Dehydrogenases with High Efficiency and Specificity toward NADP+

(2020) Liliana Calzadiaz-Ramirez et al.   ACS Catalysis

Engineering Carboxylic Acid Reductase (CAR) through a Whole-Cell Growth-Coupled NADPH Recycling Strategy

(2020) Levi Kramer et al.   ACS Synthetic Biology

Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis

(2019) William B. Black et al.   Nature Chemical Biology

Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro

(2018) Rui Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Rescue of conformational dynamics in enzyme catalysis by directed evolution

(2018) Renee Otten et al.   Nature Communications

Development of a High-Throughput, In Vivo Selection Platform for NADPH-Dependent Reactions Based on Redox Balance Principles

(2018) Linyue Zhang et al.   ACS Synthetic Biology

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Selection of an endogenous 2,3-butanediol pathway in Escherichia coli by fermentative redox balance

(2017) Keming Liang et al.   METABOLIC ENGINEERING

Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design

(2017) Lemuel M. J. Soh et al.   ACS Synthetic Biology

Enhancing the Activity of a Dietzia sp. D5 Baeyer-Villiger Monooxygenase towards Cyclohexanone by Saturation Mutagenesis

(2017) Serena Bisagni et al.   ChemistrySelect

Two strategies to engineer flexible loops for improved enzyme thermostability

(2017) Haoran Yu et al.   Scientific Reports

Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase

(2016) Elvira Romero et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

(2016) Kristoffer E. Johansson et al.   JOURNAL OF MOLECULAR BIOLOGY

Engineering of Baeyer-Villiger monooxygenase-based Escherichia coli biocatalyst for large scale biotransformation of ricinoleic acid into (Z)-11-(heptanoyloxy)undec-9-enoic acid

(2016) Joo-Hyun Seo et al.   Scientific Reports

A general and efficient strategy for generating the stable enzymes

(2016) Xiao-Fei Zhang et al.   Scientific Reports

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

The effect of disulfide bond introduction and related Cys/Ser mutations on the stability of a cyclohexanone monooxygenase

(2015) Sandy Schmidt et al.   JOURNAL OF BIOTECHNOLOGY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Lactone-Bound Structures of Cyclohexanone Monooxygenase Provide Insight into the Stereochemistry of Catalysis

(2014) Brahm J. Yachnin et al.   ACS Chemical Biology

Isobutanol production at elevated temperatures in thermophilic Geobacillus thermoglucosidasius

(2014) Paul P. Lin et al.   METABOLIC ENGINEERING

Stabilization of cyclohexanone monooxygenase by a computationally designed disulfide bond spanning only one residue

(2014) Hugo L. van Beek et al.   FEBS Open Bio

Structure- and sequence-analysis inspired engineering of proteins for enhanced thermostability

(2013) Hein J Wijma et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Blending Baeyer–Villiger monooxygenases: using a robust BVMO as a scaffold for creating chimeric enzymes with novel catalytic properties

(2012) Hugo L. van Beek et al.   CHEMICAL COMMUNICATIONS

The Substrate-Bound Crystal Structure of a Baeyer–Villiger Monooxygenase Exhibits a Criegee-like Conformation

(2012) Brahm J. Yachnin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols

(2012) Hidevaldo B. Machado et al.   METABOLIC ENGINEERING

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Automated selection of stabilizing mutations in designed and natural proteins

(2012) B. Borgo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

Evolution ofEscherichia colifor Growth at High Temperatures

(2010) Birgit Rudolph et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structures of Cyclohexanone Monooxygenase Reveal Complex Domain Movements and a Sliding Cofactor

(2009) I. Ahmad Mirza et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

Understanding and Improving NADPH-Dependent Reactions by Nongrowing Escherichia coli Cells

(2004) Adam Z. Walton et al.   BIOTECHNOLOGY PROGRESS