De novo design of a fluorescence-activating β-barrel

De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy

(2017) Nicholas F. Polizzi et al.   Nature Chemistry

Sampling and energy evaluation challenges in ligand binding protein design

(2017) Jiayi Dou et al.   PROTEIN SCIENCE

Elastic Surface Model For Beta-Barrels: Geometric, Computational, And Statistical Analysis

(2017) Magdalena Toda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Computational design of environmental sensors for the potent opioid fentanyl

(2017) Matthew J Bick et al.   eLife

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

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

Small fluorescence-activating and absorption-shifting tag for tunable protein imaging in vivo

(2015) Marie-Aude Plamont et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Origin of Consistent Protein Structure Refinement from Structural Averaging

(2015) Hahnbeom Park et al.   STRUCTURE

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

(2014) Katherine Deigan Warner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Anticalins: Exploiting a non-Ig scaffold with hypervariable loops for the engineering of binding proteins

(2013) A. Richter et al.   FEBS LETTERS

Computational Design of a Protein-Based Enzyme Inhibitor

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

Computational design of protein-small molecule interfaces

(2013) Brittany Allison et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2013) Christine E. Tinberg et al.   NATURE

Reprogramming homing endonuclease specificity through computational design and directed evolution

(2013) Summer B. Thyme et al.   NUCLEIC ACIDS RESEARCH

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Towards automated crystallographic structure refinement withphenix.refine

(2012) Pavel V. Afonine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Enrich: software for analysis of protein function by enrichment and depletion of variants

(2011) Douglas M. Fowler et al.   BIOINFORMATICS

Predicting Three-Dimensional Structures of Transmembrane Domains of β-Barrel Membrane Proteins

(2011) Hammad Naveed et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Natural tri- to hexapeptides self-assemble in water to amyloid  -type fiber aggregates by unexpected  -helical intermediate structures

(2011) C. A. E. Hauser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Excited state reactions in fluorescent proteins

(2009) Stephen R. Meech   CHEMICAL SOCIETY REVIEWS

xia2: an expert system for macromolecular crystallography data reduction

(2009) G. Winter   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY