Principles for designing proteins with cavities formed by curved β sheets

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

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

(2015) Matthew J. O’Meara et al.   Journal of Chemical Theory and Computation

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

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

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

Control over overall shape and size in de novo designed proteins

(2015) Yu-Ru Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin of β-strand bending in globular proteins

(2015) Kazuo Fujiwara et al.   BMC STRUCTURAL BIOLOGY

Design of activated serine–containing catalytic triads with atomic-level accuracy

(2014) Sridharan Rajagopalan et al.   Nature Chemical Biology

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

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

(2013) Roberto Tejero et al.   JOURNAL OF BIOMOLECULAR NMR

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

(2013) Christine E. Tinberg et al.   NATURE

Evolution of a designed retro-aldolase leads to complete active site remodeling

(2013) Lars Giger et al.   Nature Chemical Biology

Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis

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

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

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

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

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium

(2010) Rong Xiao et al.   JOURNAL OF STRUCTURAL BIOLOGY

3V: cavity, channel and cleft volume calculator and extractor

(2010) N. R. Voss et al.   NUCLEIC ACIDS RESEARCH

RosettaHoles2: A volumetric packing measure for protein structure refinement and validation

(2010) William Sheffler et al.   PROTEIN SCIENCE

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

(2010) J. B. Siegel et al.   SCIENCE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A microscale protein NMR sample screening pipeline

(2009) Paolo Rossi et al.   JOURNAL OF BIOMOLECULAR NMR

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