An Automated Flow for Directed Evolution Based on Detection of Promiscuous Scaffolds Using Spatial and Electrostatic Properties of Catalytic Residues

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

(2012) Yosephine Gumulya et al.   CHEMBIOCHEM

A Measure of the Promiscuity of Proteins and Characteristics of Residues in the Vicinity of the Catalytic Site That Regulate Promiscuity

(2012) Sandeep Chakraborty et al.   PLoS One

Functional Evolution of Duplicated Odorant-Binding Protein Genes, Obp57d and Obp57e, in Drosophila

(2012) Eriko Harada et al.   PLoS One

Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

(2012) Kirandeep Bhullar et al.   PLoS One

Circular Permutation in the Ω-Loop of TEM-1 β-Lactamase Results in Improved Activity and Altered Substrate Specificity

(2012) Gurkan Guntas et al.   PLoS One

Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

(2012) Sandeep Chakraborty   PLoS One

An engineered innate immune defense protects grapevines from Pierce disease

(2012) A. M. Dandekar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strategy and success for the directed evolution of enzymes

(2011) Paul A Dalby   CURRENT OPINION IN STRUCTURAL BIOLOGY

Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis

(2011) David P Nannemann et al.   Future Medicinal Chemistry

PBP5, PBP6 and DacD play different roles in intrinsic  -lactam resistance of Escherichia coli

(2011) S. K. Sarkar et al.   MICROBIOLOGY-SGM

A system for the continuous directed evolution of biomolecules

(2011) Kevin M. Esvelt et al.   NATURE

Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

(2011) Sandeep Chakraborty et al.   PLoS One

Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library

(2011) A. G. Sandstrom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beyond directed evolution—semi-rational protein engineering and design

(2010) Stefan Lutz   CURRENT OPINION IN BIOTECHNOLOGY

Exploiting Models of Molecular Evolution to Efficiently Direct Protein Engineering

(2010) Megan F. Cole et al.   JOURNAL OF MOLECULAR EVOLUTION

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

Development of an In Vitro Compartmentalization Screen for High-Throughput Directed Evolution of [FeFe] Hydrogenases

(2010) James A. Stapleton et al.   PLoS One

Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture

(2010) C. K. Savile et al.   SCIENCE

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

An artificial di-iron oxo-protein with phenol oxidase activity

(2009) Marina Faiella et al.   Nature Chemical Biology

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

Computational structure-based redesign of enzyme activity

(2009) C.-Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated scaffold selection for enzyme design

(2009) Christoph Malisi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A note on difficult structure alignment problems

(2008) M. J. Sippl et al.   BIOINFORMATICS

A New Family of Cyanobacterial Penicillin-binding Proteins

(2008) Carole Urbach et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

(2008) Ivelin Georgiev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure of PBP-A from Thermosynechococcus elongatus, a Penicillin-Binding Protein Closely Related to Class A β-Lactamases

(2008) Carole Urbach et al.   JOURNAL OF MOLECULAR BIOLOGY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Directed Evolution Generates a Novel Oncolytic Virus for the Treatment of Colon Cancer

(2008) Irene Kuhn et al.   PLoS One

Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration

(2008) Özlem Doğan Ekici et al.   PROTEIN SCIENCE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Physiological functions of D-alanine carboxypeptidases in Escherichia coli

(2008) Anindya S. Ghosh et al.   TRENDS IN MICROBIOLOGY

Neutrophil elastase, proteinase 3 and cathepsin G: Physicochemical properties, activity and physiopathological functions

(2007) Brice Korkmaz et al.   BIOCHIMIE