Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

Self-Assembling 2D Arrays with de Novo Protein Building Blocks

(2019) Zibo Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

De novo design of tunable, pH-driven conformational changes

(2019) Scott E. Boyken et al.   SCIENCE

De novo design of bioactive protein switches

(2019) Robert A. Langan et al.   NATURE

Chemical shift-based methods in NMR structure determination

(2018) Santrupti Nerli et al.   PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

Rational design of proteins that exchange on functional timescales

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

MetalPDB in 2018: a database of metal sites in biological macromolecular structures

(2017) Valeria Putignano et al.   NUCLEIC ACIDS RESEARCH

Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport

(2017) Nathan H. Joh et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

(2016) Dina Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

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

(2016) S. E. Boyken et al.   SCIENCE

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

(2016) Robert Lizatović et al.   STRUCTURE

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

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

Virus and Cell Fusion Mechanisms

(2014) Benjamin Podbilewicz   Annual Review of Cell and Developmental Biology

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

(2014) Woonghee Lee et al.   BIOINFORMATICS

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

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

Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates

(2013) Tijana Ivanovic et al.   eLife

Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

(2011) Nikolaos G. Sgourakis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

A Generic Program for Multistate Protein Design

(2011) Andrew Leaver-Fay et al.   PLoS One

Joint X-ray and neutron refinement withphenix.refine

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

XDS

(2010) Wolfgang Kabsch   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

Facile measurement of 1H–15N residual dipolar couplings in larger perdeuterated proteins

(2010) Nicholas C. Fitzkee et al.   JOURNAL OF BIOMOLECULAR NMR

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

Direct single-molecule observation of a protein living in two opposed native structures

(2009) Y. Gambin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A minimal sequence code for switching protein structure and function

(2009) Patrick A. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA