Evolution of chalcone isomerase from a noncatalytic ancestor

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro approach to protein engineering

(2016) Y. Gumulya et al.   BIOCHEMICAL JOURNAL

On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins

(2016) Devin L. Trudeau et al.   MOLECULAR BIOLOGY AND EVOLUTION

An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme

(2016) Mary Ortmayer et al.   NATURE

An experimental phylogeny to benchmark ancestral sequence reconstruction

(2016) Ryan N. Randall et al.   Nature Communications

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

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

The widespread role of non-enzymatic reactions in cellular metabolism

(2015) Markus A Keller et al.   CURRENT OPINION IN BIOTECHNOLOGY

Enzymatic characterization and gene identification of aconitate isomerase, an enzyme involved in assimilation oftrans-aconitic acid, fromPseudomonassp. WU-0701

(2015) Kahori Yuhara et al.   FEBS Journal

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

Role of a chalcone isomerase-like protein in flavonoid biosynthesis inArabidopsis thaliana

(2015) Wenbo Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Assessing the prediction fidelity of ancestral reconstruction by a library approach

(2015) Hagit Bar-Rogovsky et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Reverse evolution leads to genotypic incompatibility despite functional and active site convergence

(2015) Miriam Kaltenbach et al.   eLife

Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase

(2015) Maren Thomsen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Dynamics and constraints of enzyme evolution

(2014) Miriam Kaltenbach et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

A chalcone isomerase-like protein enhances flavonoid production and flower pigmentation

(2014) Yasumasa Morita et al.   PLANT JOURNAL

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution

(2013) B. C. Dickinson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering specialized metabolic pathways—is there a room for enzyme improvements?

(2012) Arren Bar-Even et al.   CURRENT OPINION IN BIOTECHNOLOGY

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis

(2012) Micheline N. Ngaki et al.   NATURE

New lives for old: evolution of pseudoenzyme function illustrated by iRhoms

(2012) Colin Adrain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Intramolecular Epistasis and the Evolution of a New Enzymatic Function

(2012) Sajid Noor et al.   PLoS One

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

(2012) O. Khersonsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM

(2011) T. Geoff G. Battye et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins

(2011) Michael Bieri et al.   JOURNAL OF BIOMOLECULAR NMR

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

The causes of epistasis

(2011) J. A. G. M. de Visser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Conformational diversity and computational enzyme design

(2010) Jonathan K Lassila   CURRENT OPINION IN CHEMICAL BIOLOGY

The origin and evolution of lignin biosynthesis

(2010) Jing-Ke Weng et al.   NEW PHYTOLOGIST

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers

(2009) Henry van den Bedem et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

(2009) E. R. Lozovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA