How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiency

(2020) Hajo Kries et al.   ACS Catalysis

A Universal Quantitative Descriptor of Dispersive Interaction Potential

(2019) Robert Pollice et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Role of conformational dynamics in the evolution of novel enzyme function

(2018) Miguel A. Maria-Solano et al.   CHEMICAL COMMUNICATIONS

Laboratory evolution of protein conformational dynamics

(2018) Eleanor C Campbell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The evolution of multiple active site configurations in a designed enzyme

(2018) Nan-Sook Hong et al.   Nature Communications

Comprehensive analysis of NMR data using advanced line shape fitting

(2017) Markus Niklasson et al.   JOURNAL OF BIOMOLECULAR NMR

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

(2017) Harry C Jubb et al.   JOURNAL OF MOLECULAR BIOLOGY

CheckMyMetal: a macromolecular metal-binding validation tool

(2017) Heping Zheng et al.   Acta Crystallographica Section D-Structural Biology

Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase

(2016) Richard Obexer et al.   Nature Chemistry

Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies

(2014) Amnon Kohen   ACCOUNTS OF CHEMICAL RESEARCH

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

(2014) Woonghee Lee et al.   BIOINFORMATICS

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

(2014) N. Preiswerk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell

(2014) Marcin Kowiel et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

How good are my data and what is the resolution?

(2013) Philip R. Evans et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Nmrglue: an open source Python package for the analysis of multidimensional NMR data

(2013) Jonathan J. Helmus et al.   JOURNAL OF BIOMOLECULAR NMR

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

emcee: The MCMC Hammer

(2013) Daniel Foreman-Mackey et al.   PUBLICATIONS OF THE ASTRONOMICAL SOCIETY OF THE PACIFIC

Statistical quality indicators for electron-density maps

(2012) Ian J. Tickle   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Optimal simultaneous superpositioning of multiple structures with missing data

(2012) Douglas L. Theobald et al.   BIOINFORMATICS

The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure

(2012) Christopher C. Valley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Modelling dynamics in protein crystal structures by ensemble refinement

(2012) B Tom Burnley et al.   eLife

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

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

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Design of a switchable eliminase

(2011) I. V. Korendovych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

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

Coupled motions in enzyme catalysis

(2010) Vishal C Nashine et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

(2009) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series

(2009) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology

FitSpace Explorer: An algorithm to evaluate multidimensional parameter space in fitting kinetic data

(2008) Kenneth A. Johnson et al.   ANALYTICAL BIOCHEMISTRY

Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data

(2008) Kenneth A. Johnson et al.   ANALYTICAL BIOCHEMISTRY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE