Learning epistatic interactions from sequence-activity data to predict enantioselectivity

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

(2017) Claire N. Bedbrook et al.   PLoS Computational Biology

New Concepts for Increasing the Efficiency in Directed Evolution of Stereoselective Enzymes

(2016) Zhoutong Sun et al.   CHEMISTRY-A EUROPEAN JOURNAL

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

How mutational epistasis impairs predictability in protein evolution and design

(2016) Charlotte M. Miton et al.   PROTEIN SCIENCE

Enantioselective Enzymes by Computational Design and In Silico Screening

(2015) Hein J. Wijma et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Topological features of rugged fitness landscapes in sequence space

(2015) Dmitry A. Kondrashov et al.   TRENDS IN GENETICS

Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations

(2014) Hein J. Wijma et al.   Journal of Chemical Information and Modeling

“New Drug” Designations for New Therapeutic Entities: New Active Substance, New Chemical Entity, New Biological Entity, New Molecular Entity

(2014) Sarah K. Branch et al.   JOURNAL OF MEDICINAL CHEMISTRY

Protein redesign by learning from data

(2014) Bastiaan A. van den Berg et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Predicting CYP2C19 catalytic parameters for enantioselective oxidations using artificial neural networks and a chirality code

(2013) Jessica H. Hartman et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Many Pathways in Laboratory Evolution Can Lead to Improved Enzymes: How to Escape from Local Minima

(2012) Yosephine Gumulya et al.   CHEMBIOCHEM

Enhancing the Efficiency of Directed Evolution in Focused Enzyme Libraries by the Adaptive Substituent Reordering Algorithm

(2012) Xiaojiang Feng et al.   CHEMISTRY-A EUROPEAN JOURNAL

A diverse set of family 48 bacterial glycoside hydrolase cellulases created by structure-guided recombination

(2012) Matthew A. Smith et al.   FEBS Journal

Engineering the third wave of biocatalysis

(2012) U. T. Bornscheuer et al.   NATURE

The predicated demise of racemic new molecular entities is an exaggeration

(2012) Israel Agranat et al.   NATURE REVIEWS DRUG DISCOVERY

SCHEMA-Designed Variants of Human Arginase I and II Reveal Sequence Elements Important to Stability and Catalysis

(2012) Philip A. Romero et al.   ACS Synthetic Biology

Random Field Model Reveals Structure of the Protein Recombinational Landscape

(2012) Philip A. Romero et al.   PLoS Computational Biology

Quantitative prediction of enantioselectivity of Candida antarctica lipase B by combining docking simulations and quantitative structure–activity relationship (QSAR) analysis

(2011) Jiali Gu et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

Contribution of both catalytic constant and Michaelis constant to CALB enantioselectivity: Use of FEP calculations for prediction studies

(2011) L. Chaput et al.   JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC

Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets

(2010) Gerard J. P. van Westen et al.   MedChemComm

A Three-Dimensional Quanititative Structure-Activity Relationship (3D-QSAR) Model for Predicting the Enantioselectivity ofCandida antarcticaLipase B

(2009) Paolo Braiuca et al.   ADVANCED SYNTHESIS & CATALYSIS

Highly Enantioselective Reduction of a Small Heterocyclic Ketone: Biocatalytic Reduction of Tetrahydrothiophene-3-one to the Corresponding (R)-Alcohol

(2009) Jack Liang et al.   ORGANIC PROCESS RESEARCH & DEVELOPMENT

A family of thermostable fungal cellulases created by structure-guided recombination

(2009) P. Heinzelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In silico characterization of protein chimeras: Relating sequence and function within the same fold

(2009) Fabian A. Buske et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Constructing and Analyzing the Fitness Landscape of an Experimental Evolutionary Process

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

A comprehensive analysis of the thermodynamic events involved in ligand–receptor binding using CoRIA and its variants

(2008) Jitender Verma et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology