Why reinvent the wheel? Building new proteins based on ready-made parts

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

(2015) Po-Ssu Huang et al.   Nature Chemical Biology

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

(2015) Gideon D. Lapidoth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design of proteins from smaller fragments—learning from evolution

(2014) Birte Höcker   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evolutionary relationship of two ancient protein superfolds

(2014) José Arcadio Farías-Rico et al.   Nature Chemical Biology

Computational design of a pH-sensitive IgG binding protein

(2014) E.-M. Strauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Global view of the protein universe

(2014) S. Nepomnyachiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

(2013) Zhixiu Li et al.   Annual Review of Biophysics

Establishing catalytic activity on an artificial (βα)8 -barrel protein designed from identical half-barrels

(2013) Josef M. Sperl et al.   FEBS LETTERS

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Design of a Protein-Based Enzyme Inhibitor

(2013) Erik Procko et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2013) Christine E. Tinberg et al.   NATURE

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Octarellin VI: Using Rosetta to Design a Putative Artificial (β/α)8 Protein

(2013) Maximiliano Figueroa et al.   PLoS One

Reconstructing a Missing Link in the Evolution of a Recently Diverged Phosphotriesterase by Active-Site Loop Remodeling

(2012) Livnat Afriat-Jurnou et al.   BIOCHEMISTRY

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

(2012) Sarel J. Fleishman et al.   CELL

Directed enzyme evolution: beyond the low-hanging fruit

(2012) Moshe Goldsmith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Potential of Fragment Recombination for Rational Design of Proteins

(2012) Simone Eisenbeis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

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

A highly stable protein chimera built from fragments of different folds

(2012) S. Shanmugaratnam et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Experimental support for the foldability-function tradeoff hypothesis: Segregation of the folding nucleus and functional regions in fibroblast growth factor-1

(2012) Liam Longo et al.   PROTEIN SCIENCE

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

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

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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Restricted sidechain plasticity in the structures of native proteins and complexes

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

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

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

Computational and Experimental Evidence for the Evolution of a (βα)8-Barrel Protein from an Ancestral Quarter-Barrel Stabilised by Disulfide Bonds

(2010) Markus Richter et al.   JOURNAL OF MOLECULAR BIOLOGY

Metamorphic proteins mediate evolutionary transitions of structure

(2010) I. Yadid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental support for the evolution of symmetric protein architecture from a simple peptide motif

(2010) J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional β-propeller lectins by tandem duplications of repetitive units

(2010) Itamar Yadid et al.   PROTEIN ENGINEERING DESIGN & SELECTION

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Establishing wild-type levels of catalytic activity on natural and artificial (  )8-barrel protein scaffolds

(2009) J. Claren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental Evidence for the Existence of a Stable Half-Barrel Subdomain in the (β/α)8-Barrel Fold

(2008) Satoshi Akanuma et al.   JOURNAL OF MOLECULAR BIOLOGY

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology

Evolution of the β-propeller fold

(2007) Indronil Chaudhuri et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS