Protein design: Past, present, and future

Designed Phosphoprotein Recognition in Escherichia coli

(2014) Nicholas Sawyer et al.   ACS Chemical Biology

Structure of a designed protein cage that self-assembles into a highly porous cube

(2014) Yen-Ting Lai et al.   Nature Chemistry

Synthesis of bioactive protein hydrogels by genetically encoded SpyTag-SpyCatcher chemistry

(2014) F. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic α-helical and β-sheet conformational preferences: A computational case study of alanine

(2014) Diego Caballero et al.   PROTEIN SCIENCE

Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

(2014) Alice Qinhua Zhou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

New Insights into the Interdependence between Amino Acid Stereochemistry and Protein Structure

(2013) Alice Qinhua Zhou et al.   BIOPHYSICAL JOURNAL

Fluorescent proteins for live-cell imaging with super-resolution

(2013) Karin Nienhaus et al.   CHEMICAL SOCIETY REVIEWS

An Engineered Monomeric Zoanthus sp. Yellow Fluorescent Protein

(2013) Hiofan Hoi et al.   CHEMISTRY & BIOLOGY

A LOV2 Domain-Based Optogenetic Tool to Control Protein Degradation and Cellular Function

(2013) Christian Renicke et al.   CHEMISTRY & BIOLOGY

Controlling Macromolecular Topology with Genetically Encoded SpyTag–SpyCatcher Chemistry

(2013) Wen-Bin Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments

(2013) Helena Gradišar et al.   Nature Chemical Biology

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Self-Assembling Cages from Coiled-Coil Peptide Modules

(2013) J. M. Fletcher et al.   SCIENCE

The Power of Hard-Sphere Models: Explaining Side-Chain Dihedral Angle Distributions of Thr and Val

(2012) Alice Qinhua Zhou et al.   BIOPHYSICAL JOURNAL

A modular approach to the design of protein-based smart gels

(2012) Tijana Z. Grove et al.   BIOPOLYMERS

Chromophore Transformations in Red Fluorescent Proteins

(2012) Fedor V. Subach et al.   CHEMICAL REVIEWS

Intrinsic Energy Landscapes of Amino Acid Side-Chains

(2012) Xiao Zhu et al.   Journal of Chemical Information and Modeling

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Critical Assessment of Current Force Fields. Short Peptide Test Case

(2012) Jiří Vymětal et al.   Journal of Chemical Theory and Computation

TULIPs: tunable, light-controlled interacting protein tags for cell biology

(2012) Devin Strickland et al.   NATURE METHODS

Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin

(2012) B. Zakeri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Computational design of a protein crystal

(2012) C. J. Lanci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

(2012) P. Benjamin Stranges et al.   PROTEIN SCIENCE

Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%

(2012) Joachim Goedhart et al.   Nature Communications

SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains

(2012) Kenneth Evan Thompson et al.   ACS Synthetic Biology

DNA Origami: The Art of Folding DNA

(2011) Barbara Saccà et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Design of a β-Peptide That Targets Transmembrane Helices

(2011) Scott J. Shandler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bright and stable near-infrared fluorescent protein for in vivo imaging

(2011) Grigory S Filonov et al.   NATURE BIOTECHNOLOGY

Design of a switchable eliminase

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

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

Expanding the Genetic Code of Escherichia coli with Phosphoserine

(2011) H.-S. Park et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Rapid Inactivation of Proteins by Rapamycin-Induced Rerouting to Mitochondria

(2010) Margaret S. Robinson et al.   DEVELOPMENTAL CELL

A new bright green-emitting fluorescent protein - engineered monomeric and dimeric forms

(2010) Robielyn P. Ilagan et al.   FEBS Journal

Determination of Isoleucine Side-Chain Conformations in Ground and Excited States of Proteins from Chemical Shifts

(2010) D. Flemming Hansen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stimuli-Responsive Smart Gels Realized via Modular Protein Design

(2010) Tijana Z. Grove et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Yielding Behavior in Injectable Hydrogels from Telechelic Proteins

(2010) Bradley D. Olsen et al.   MACROMOLECULES

Near-infrared fluorescent proteins

(2010) Dmitry Shcherbo et al.   NATURE METHODS

Creating novel proteins by combining design and selection

(2010) T. Z. Grove et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Protein design automation

(2010) Bassil I. Dahiyat et al.   PROTEIN SCIENCE

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

(2010) J. B. Siegel et al.   SCIENCE

Designed Proteins To Modulate Cellular Networks

(2009) Aitziber L. Cortajarena et al.   ACS Chemical Biology

Designs and applications of fluorescent protein-based biosensors

(2009) Andreas Ibraheem et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Intrinsic Propensities of Amino Acid Residues in GxG Peptides Inferred from Amide I′ Band Profiles and NMR Scalar Coupling Constants

(2009) Andrew Hagarman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determination of Leu Side-Chain Conformations in Excited Protein States by NMR Relaxation Dispersion

(2009) D. Flemming Hansen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

Rational design and application of responsive α-helical peptide hydrogels

(2009) Eleanor F. Banwell et al.   NATURE MATERIALS

Engineered fluorescent proteins: innovations and applications

(2009) Michael W Davidson et al.   NATURE METHODS

Algorithm for backrub motions in protein design

(2008) I. Georgiev et al.   BIOINFORMATICS

Ligand binding by repeat proteins: natural and designed

(2008) T GROVE et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability

(2008) Gregory D. Friedland et al.   JOURNAL OF MOLECULAR BIOLOGY

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