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

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

(2012) Sarel J. Fleishman et al.   CELL

Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

(2012) Katelyn Deckert et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

(2012) Florian Richter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

(2012) Christopher B Eiben et al.   NATURE BIOTECHNOLOGY

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

(2012) Sagar D Khare et al.   Nature Chemical Biology

Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays

(2012) Jeffrey D. Brodin et al.   Nature Chemistry

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

(2012) G. T. Kapp 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

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

Robust design and optimization of retroaldol enzymes

(2012) Eric A. Althoff 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

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

(2012) N. P. King et al.   SCIENCE

Principles for designing ordered protein assemblies

(2012) Yen-Ting Lai et al.   TRENDS IN CELL BIOLOGY

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

(2011) Vern L. Schramm   Annual Review of Biochemistry

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis

(2011) Maria P. Frushicheva et al.   BIOCHEMISTRY

Hotspot-Centric De Novo Design of Protein Binders

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

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR 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 Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Computational design of a symmetric homodimer using  -strand assembly

(2011) P. B. Stranges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restricted sidechain plasticity in the structures of native proteins and complexes

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

Structure-guided forcefield optimization

(2011) Yifan Song et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Computational Design of a PAK1 Binding Protein

(2010) Ramesh K. Jha et al.   JOURNAL OF MOLECULAR BIOLOGY

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

(2010) M. P. Frushicheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins of catalysis by computationally designed retroaldolase enzymes

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

Protein design automation

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

Evaluation and ranking of enzyme designs

(2010) Gert Kiss et al.   PROTEIN SCIENCE

An exciting but challenging road ahead for computational enzyme design

(2010) David Baker   PROTEIN SCIENCE

Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series

(2009) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational design of second-site suppressor mutations at protein-protein interfaces

(2009) Deanne W. Sammond et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination

(2008) Anastassia N. Alexandrova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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