De novo design of transmembrane β barrels

Rapid fabrication of precise high-throughput filters from membrane protein nanosheets

(2020) Yu-Ming Tu et al.   NATURE MATERIALS

Role of the lipid bilayer in outer membrane protein folding in Gram-negative bacteria

(2020) Jim E. Horne et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

Modular and tunable biological feedback control using a de novo protein switch

(2019) Andrew H. Ng et al.   NATURE

De novo design of bioactive protein switches

(2019) Robert A. Langan et al.   NATURE

Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

(2018) Meghan Whitney Franklin et al.   JOURNAL OF MOLECULAR BIOLOGY

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

De novo design of a non-local β-sheet protein with high stability and accuracy

(2018) Enrique Marcos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins

(2017) Marcin Michalik et al.   PLoS One

PDBsum: Structural summaries of PDB entries

(2017) Roman A. Laskowski et al.   PROTEIN SCIENCE

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Protein charge distribution in proteomes and its impact on translation

(2017) Rodrigo D. Requião et al.   PLoS Computational Biology

Novel Kinetic Intermediates Populated along the Folding Pathway of the Transmembrane β-Barrel OmpA

(2016) Emily J. Danoff et al.   BIOCHEMISTRY

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

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

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

(2016) S. E. Boyken et al.   SCIENCE

Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles

(2015) Michael T. Marty et al.   ANALYTICAL CHEMISTRY

Folding of β -barrel membrane proteins in lipid bilayers — Unassisted and assisted folding and insertion

(2015) Jörg H. Kleinschmidt   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

(2015) James A. Stapleton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Folding membrane proteins in vitro: A table and some comments

(2014) Jean-Luc Popot   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

PASTA 2.0: an improved server for protein aggregation prediction

(2014) Ian Walsh et al.   NUCLEIC ACIDS RESEARCH

Local sequence of protein β-strands influences twist and bend angles

(2014) Kazuo Fujiwara et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A mortise–tenon joint in the transmembrane domain modulates autotransporter assembly into bacterial outer membranes

(2014) Denisse L. Leyton et al.   Nature Communications

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

(2013) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm

(2013) C. Preston Moon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

β-bulges: Extensive structural analyses of β-sheets irregularities

(2013) Pierrick Craveur et al.   PROTEIN SCIENCE

Real-Time Sensing and Discrimination of Single Chemicals Using the Channel of Phi29 DNA Packaging Nanomotor

(2012) Farzin Haque et al.   ACS Nano

OmpA can form folded and unfolded oligomers

(2012) H. Wang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Sarel J. Fleishman et al.   CELL

Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling

(2012) Sven G. Hyberts et al.   JOURNAL OF BIOMOLECULAR NMR

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The soluble, periplasmic domain of OmpA folds as an independent unit and displays chaperone activity by reducing the self-association propensity of the unfolded OmpA transmembrane β-barrel

(2011) Emily J. Danoff et al.   BIOPHYSICAL CHEMISTRY

Overcoming Hysteresis to Attain Reversible Equilibrium Folding for Outer Membrane Phospholipase A in Phospholipid Bilayers

(2011) C. Preston Moon et al.   JOURNAL OF MOLECULAR BIOLOGY

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

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

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Self-Association of Unfolded Outer Membrane Proteins

(2010) Alexandra Ebie Tan et al.   MACROMOLECULAR BIOSCIENCE

The transition state for folding of an outer membrane protein

(2010) G. H. M. Huysmans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

(2009) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

β-Barrel Proteins That Reside in theEscherichia coliOuter Membranein VivoDemonstrate Varied Folding Behaviorin Vitro

(2008) Nancy K. Burgess et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-molecule DNA detection with an engineered MspA protein nanopore

(2008) T. Z. Butler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily

(2002) Lesley H. Greene et al.   PROTEIN SCIENCE

Toward genomic identification of β-barrel membrane proteins: Composition and architecture of known structures

(2002) William C. Wimley   PROTEIN SCIENCE