De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity

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

DNA nanotechnology from the test tube to the cell

(2015) Yuan-Jyue Chen et al.   Nature Nanotechnology

Hydrogen Bonding Networks Tune Proton-Coupled Redox Steps during the Enzymatic Six-Electron Conversion of Nitrite to Ammonia

(2014) Evan T. Judd et al.   BIOCHEMISTRY

Structural DNA Nanotechnology: State of the Art and Future Perspective

(2014) Fei Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Increasing the affinity of selective bZIP-binding peptides through surface residue redesign

(2014) Jenifer B. Kaplan et al.   PROTEIN SCIENCE

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

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

(2013) Dina Schneidman-Duhovny et al.   BIOPHYSICAL JOURNAL

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

(2013) Shintaro Minami et al.   BMC BIOINFORMATICS

Computational Design of a Protein-Based Enzyme Inhibitor

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

A Set of de Novo Designed Parallel Heterodimeric Coiled Coils with Quantified Dissociation Constants in the Micromolar to Sub-nanomolar Regime

(2013) Franziska Thomas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution

(2013) A. W. Reinke et al.   SCIENCE

Complex shapes self-assembled from single-stranded DNA tiles

(2012) Bryan Wei et al.   NATURE

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

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

De novo designed peptides for biological applications

(2011) Aimee L. Boyle et al.   CHEMICAL SOCIETY REVIEWS

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

Modeling Symmetric Macromolecular Structures in Rosetta3

(2011) Frank DiMaio et al.   PLoS One

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

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

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Computational protein design with explicit consideration of surface hydrophobic patches

(2011) Ron Jacak 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

Joint X-ray and neutron refinement withphenix.refine

(2010) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

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

Scatter: software for the analysis of nano- and mesoscale small-angle scattering

(2010) S. Förster et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Probing Designability via a Generalized Model of Helical Bundle Geometry

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

De novo design of orthogonal peptide pairs forming parallel coiled-coil heterodimers

(2010) Helena Gradišar et al.   JOURNAL OF PEPTIDE SCIENCE

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

(2010) Aaron W. Reinke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

The crystal structure of the designed trimeric coiled coil coil-VaLd: Implications for engineering crystals and supramolecular assemblies

(2010) Nancy L. Ogihara et al.   PROTEIN SCIENCE

Protein design automation

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

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

(2009) Gevorg Grigoryan et al.   NATURE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Simultaneous prediction of protein folding and docking at high resolution

(2009) Rhiju Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural specificity in coiled-coil interactions

(2008) G GRIGORYAN et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY