Sampling and energy evaluation challenges in ligand binding protein design

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

(2016) S. E. Boyken et al.   SCIENCE

A general strategy to construct small molecule biosensors in eukaryotes

(2015) Justin Feng et al.   eLife

Bioluminescent sensor proteins for point-of-care therapeutic drug monitoring

(2014) Rudolf Griss et al.   Nature Chemical Biology

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

(2013) J. Zhang et al.   BIOINFORMATICS

Computational Design of a Protein-Based Enzyme Inhibitor

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

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

(2013) Christine E. Tinberg et al.   NATURE

Small-molecule ligand docking into comparative models with Rosetta

(2013) Steven A Combs et al.   Nature Protocols

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

(2013) Lucas Gregorio Nivón et al.   PLoS One

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

(2012) Vahid Mirjalili et al.   Journal of Chemical Theory and Computation

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

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

(2011) Douglas M. Fowler et al.   BIOINFORMATICS

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

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

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Restricted sidechain plasticity in the structures of native proteins and complexes

(2011) Sarel J. Fleishman et al.   PROTEIN SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

An improved yeast transformation method for the generation of very large human antibody libraries

(2010) Lorenzo Benatuil et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Neonatal screening for congenital adrenal hyperplasia

(2009) Perrin C. White   Nature Reviews Endocrinology

Crystal structure of Mycobacterium tuberculosis Rv0760c at 1.50 Å resolution, a structural homolog of Δ5-3-ketosteroid isomerase

(2008) Maia M. Cherney et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS