Machine learning-assisted directed protein evolution with combinatorial libraries

Directed Evolution of Protein Catalysts

(2018) Cathleen Zeymer et al.   Annual Review of Biochemistry

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Improved Descriptors for the Quantitative Structure–Activity Relationship Modeling of Peptides and Proteins

(2018) Mark H. Barley et al.   Journal of Chemical Information and Modeling

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Catalytic iron-carbene intermediate revealed in a cytochromeccarbene transferase

(2018) Russell D. Lewis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ProtaBank: A repository for protein design and engineering data

(2018) Connie Y. Wang et al.   PROTEIN SCIENCE

Molecular modeling of conformational dynamics and its role in enzyme evolution

(2018) Petrović Dušan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated Design of Efficient and Functionally Diverse Enzyme Repertoires

(2018) Olga Khersonsky et al.   MOLECULAR CELL

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins

(2018) Yutaka Saito et al.   ACS Synthetic Biology

Enzymatic assembly of carbon–carbon bonds via iron-catalysed sp3 C–H functionalization

(2018) Ruijie K. Zhang et al.   NATURE

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes

(2018) Frédéric Cadet et al.   Scientific Reports

CADEE: Computer-Aided Directed Evolution of Enzymes

(2017) Beat Anton Amrein et al.   IUCrJ

Copper-catalysed enantioselective stereodivergent synthesis of amino alcohols

(2016) Shi-Liang Shi et al.   NATURE

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life

(2016) S. B. Jennifer Kan et al.   SCIENCE

Adaptation in protein fitness landscapes is facilitated by indirect paths

(2016) Nicholas C Wu et al.   eLife

Environmental changes bridge evolutionary valleys

(2016) B. Steinberg et al.   Science Advances

Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants

(2016) Dylan Alexander Carlin et al.   PLoS One

Machine learning: Trends, perspectives, and prospects

(2015) M. I. Jordan et al.   SCIENCE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

SwiftLib: rapid degenerate-codon-library optimization through dynamic programming

(2014) Timothy M. Jacobs et al.   NUCLEIC ACIDS RESEARCH

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

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

(2013) David E. Kim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Enantiomeric Natural Products: Occurrence and Biogenesis

(2012) Jennifer M. Finefield et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Organosilicon Molecules with Medicinal Applications

(2012) Annaliese K. Franz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Reducing Codon Redundancy and Screening Effort of Combinatorial Protein Libraries Created by Saturation Mutagenesis

(2012) Sabrina Kille et al.   ACS Synthetic Biology

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

Exploring protein fitness landscapes by directed evolution

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

Addressing the Numbers Problem in Directed Evolution

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM