A Brief History of De Novo Protein Design: Minimal, Rational, and Computational

Bottom-up de novo design of functional proteins with complex structural features

(2021) Che Yang et al.   Nature Chemical Biology

De novo design of transmembrane β barrels

(2021) Anastassia A. Vorobieva et al.   SCIENCE

De novo design of a reversible phosphorylation-dependent switch for membrane targeting

(2021) Leon Harrington et al.   Nature Communications

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins

(2021) Jason C. Klima et al.   Nature Communications

Structural resolution of switchable states of a de novo peptide assembly

(2021) William M. Dawson et al.   Nature Communications

100th Anniversary of Macromolecular Science Viewpoint: Data-Driven Protein Design

(2021) Andrew L. Ferguson et al.   ACS Macro Letters

Designing better enzymes: Insights from directed evolution

(2021) H. Adrian Bunzel et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A biosensor for the direct visualization of auxin

(2021) Ole Herud-Sikimić et al.   NATURE

Constructing ion channels from water-soluble α-helical barrels

(2021) Alistair J. Scott et al.   Nature Chemistry

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Rosetta and the journey to predict proteins’ structures, 20 years on

(2020) Jad Abbass et al.   Current Bioinformatics

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

De novo protein design enables the precise induction of RSV-neutralizing antibodies

(2020) Fabian Sesterhenn et al.   SCIENCE

Computational design of transmembrane pores

(2020) Chunfu Xu et al.   NATURE

Expanding the space of protein geometries by computational design of de novo fold families

(2020) Xingjie Pan et al.   SCIENCE

A defined structural unit enables de novo design of small-molecule–binding proteins

(2020) Nicholas F. Polizzi et al.   SCIENCE

Designed protein logic to target cells with precise combinations of surface antigens

(2020) Marc J. Lajoie et al.   SCIENCE

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

(2020) Longxing Cao et al.   SCIENCE

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

(2020) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1

(2019) Vincent Frappier et al.   STRUCTURE

Packing of apolar side chains enables accurate design of highly stable membrane proteins

(2019) Marco Mravic et al.   SCIENCE

What has de novo protein design taught us about protein folding and biophysics?

(2019) David Baker   PROTEIN SCIENCE

AlphaFold at CASP13

(2019) Mohammed AlQuraishi   BIOINFORMATICS

Navigating the structural landscape of de novo α-helical bundles

(2019) Guto G. Rhys et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

De novo design of tunable, pH-driven conformational changes

(2019) Scott E. Boyken et al.   SCIENCE

Positive multistate protein design

(2019) Jelena Vucinic et al.   BIOINFORMATICS

De novo protein design by citizen scientists

(2019) Brian Koepnick et al.   NATURE

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs

(2019) Spencer A. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering Metalloprotein Functions in Designed and Native Scaffolds

(2019) Flavia Nastri et al.   TRENDS IN BIOCHEMICAL SCIENCES

Designing minimalist membrane proteins

(2019) Paul Curnow   BIOCHEMICAL SOCIETY TRANSACTIONS

Towards functional de novo designed proteins

(2019) William M Dawson et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational design of a modular protein sense-response system

(2019) Anum A. Glasgow et al.   SCIENCE

Directed Evolution of Protein Catalysts

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

Coiled coil protein origami: from modular design principles towards biotechnological applications

(2018) Fabio Lapenta et al.   CHEMICAL SOCIETY REVIEWS

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

De Novo-Designed α-Helical Barrels as Receptors for Small Molecules

(2018) Franziska Thomas et al.   ACS Synthetic Biology

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture

(2018) Mohammad ElGamacy et al.   ACS Synthetic Biology

OSPREY 3.0: Open-source protein redesign for you, with powerful new features

(2018) Mark A. Hallen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evolution of a highly active and enantiospecific metalloenzyme from short peptides

(2018) Sabine Studer et al.   SCIENCE

Maintaining and breaking symmetry in homomeric coiled-coil assemblies

(2018) Guto G. Rhys et al.   Nature Communications

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Extremozymes: A Potential Source for Industrial Applications

(2017) Kelly Dumorne; et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Engineering protein stability with atomic precision in a monomeric miniprotein

(2017) Emily G Baker et al.   Nature Chemical Biology

Rational design of proteins that exchange on functional timescales

(2017) James A Davey et al.   Nature Chemical Biology

De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy

(2017) Nicholas F. Polizzi et al.   Nature Chemistry

Membrane-spanning α-helical barrels as tractable protein-design targets

(2017) Ai Niitsu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Zinc-binding structure of a catalytic amyloid from solid-state NMR

(2017) Myungwoon Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CCBuilder 2.0: Powerful and accessible coiled-coil modeling

(2017) Christopher W. Wood et al.   PROTEIN SCIENCE

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Coiled Coils – A Model System for the 21st Century

(2017) Andrei N. Lupas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme

(2017) Daniel W. Watkins et al.   Nature Communications

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

Accurate de novo design of hyperstable constrained peptides

(2016) Gaurav Bhardwaj et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Computational design of self-assembling cyclic protein homo-oligomers

(2016) Jorge A. Fallas et al.   Nature Chemistry

Installing hydrolytic activity into a completely de novo protein framework

(2016) Antony J. Burton et al.   Nature Chemistry

Tertiary alphabet for the observable protein structural universe

(2016) Craig O. Mackenzie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consensus protein design

(2016) Benjamin T. Porebski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch

(2016) Robert Lizatović et al.   STRUCTURE

Designed Ankyrin Repeat Proteins (DARPins): Binding Proteins for Research, Diagnostics, and Therapy

(2015) Andreas Plückthun   Annual Review of Pharmacology and Toxicology

Protein design: Past, present, and future

(2015) Lynne Regan et al.   BIOPOLYMERS

De novo protein design: how do we expand into the universe of possible protein structures?

(2015) Derek N Woolfson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rational design of α-helical tandem repeat proteins with closed architectures

(2015) Lindsey Doyle et al.   NATURE

Exploring the repeat protein universe through computational protein design

(2015) TJ Brunette et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Structural and dynamic properties that govern the stability of an engineered fibronectin type III domain

(2015) Benjamin T. Porebski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

(2014) C. W. Wood et al.   BIOINFORMATICS

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

(2014) Erik Procko et al.   CELL

Protein Design: Toward Functional Metalloenzymes

(2014) Fangting Yu et al.   CHEMICAL REVIEWS

A protein engineered to bind uranyl selectively and with femtomolar affinity

(2014) Lu Zhou et al.   Nature Chemistry

Computational design of a self-assembling symmetrical β-propeller protein

(2014) Arnout R. D. Voet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

An artificial PPR scaffold for programmable RNA recognition

(2014) Sandrine Coquille et al.   Nature Communications

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Elementary tetrahelical protein design for diverse oxidoreductase functions

(2013) Tammer A Farid et al.   Nature Chemical Biology

Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein

(2013) L. M. Longo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

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

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

Artificial proteins from combinatorial approaches

(2012) Agathe Urvoas et al.   TRENDS IN BIOTECHNOLOGY

A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

(2012) Jordan M. Fletcher et al.   ACS Synthetic Biology

Tandem repeats in proteins: From sequence to structure

(2011) Andrey V. Kajava   JOURNAL OF STRUCTURAL BIOLOGY

Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer

(2011) Bryan S. Der et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A de novo peptide hexamer with a mutable channel

(2011) Nathan R Zaccai et al.   Nature Chemical Biology

Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats

(2010) Agathe Urvoas et al.   JOURNAL OF MOLECULAR BIOLOGY

Consensus Protein Design without Phylogenetic Bias

(2010) Christian Jäckel et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR BIOLOGY

Predicting protein structures with a multiplayer online game

(2010) Seth Cooper et al.   NATURE

Crystal structure of a designed, thermostable, heterotrimeric coiled coil

(2010) Shivani Nautiyal et al.   PROTEIN SCIENCE

Protein design automation

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

Design and engineering of an O2 transport protein

(2009) Ronald L. Koder et al.   NATURE

Designing artificial enzymes by intuition and computation

(2009) Vikas Nanda et al.   Nature Chemistry

Rational design and application of responsive α-helical peptide hydrogels

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Probing the “Dark Matter” of Protein Fold Space

(2009) William R. Taylor et al.   STRUCTURE

CC+: a relational database of coiled-coil structures

(2008) O. D. Testa et al.   NUCLEIC ACIDS RESEARCH

Coiled-Coil Irregularities and Instabilities in Group A Streptococcus M1 Are Required for Virulence

(2008) C. McNamara et al.   SCIENCE