Computational design of ligand-binding proteins with high affinity and selectivity

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

Emerging themes in the computational design of novel enzymes and protein-protein interfaces

(2012) Sagar D. Khare et al.   FEBS LETTERS

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

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

Enrich: software for analysis of protein function by enrichment and depletion of variants

(2011) Douglas M. Fowler et al.   BIOINFORMATICS

Vaccines Against Drug Abuse

(2011) X Y Shen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Structural Analyses of Covalent Enzyme–Substrate Analog Complexes Reveal Strengths and Limitations of De Novo Enzyme Design

(2011) Ling Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

Beyond natural antibodies: the power of in vitro display technologies

(2011) Andrew R M Bradbury et al.   NATURE BIOTECHNOLOGY

Analysis of protein-ligand interactions by fluorescence polarization

(2011) Ana M Rossi et al.   Nature Protocols

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

(2011) Sarel J. Fleishman et al.   PLoS One

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Restricted sidechain plasticity in the structures of native proteins and complexes

(2011) Sarel J. Fleishman et al.   PROTEIN SCIENCE

Optimizing non-natural protein function with directed evolution

(2010) Eric M Brustad et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

An improved yeast transformation method for the generation of very large human antibody libraries

(2010) Lorenzo Benatuil et al.   PROTEIN ENGINEERING DESIGN & SELECTION

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2010) J. B. Siegel et al.   SCIENCE

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Computational design of ligand binding is not a solved problem

(2009) B. Schreier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE