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

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

(2017) Pascal Leuenberger 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

Accurate de novo design of hyperstable constrained peptides

(2016) Gaurav Bhardwaj et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

(2016) Vikram Alva et al.   NUCLEIC ACIDS RESEARCH

Protein engineering by highly parallel screening of computationally designed variants

(2016) M. G. F. Sun et al.   Science Advances

Protein stability: computation, sequence statistics, and new experimental methods

(2015) Thomas J Magliery   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fluorescence Correlation Spectroscopy Reveals Highly Efficient Cytosolic Delivery of Certain Penta-Arg Proteins and Stapled Peptides

(2015) Jonathan R. LaRochelle et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Local and macroscopic electrostatic interactions in single α-helices

(2015) Emily G Baker et al.   Nature Chemical Biology

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

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

(2015) Fan Zheng et al.   STRUCTURE

Learning Bayesian Networks with thebnlearnRPackage

(2015) Marco Scutari   Journal of Statistical Software

Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion

(2014) Yanbo Pan et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Forces stabilizing proteins

(2014) C. Nick Pace et al.   FEBS LETTERS

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

(2014) Hai Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

Contribution of hydrogen bonds to protein stability

(2014) C. Nick Pace et al.   PROTEIN SCIENCE

Fast protein folding kinetics

(2014) Hannah Gelman et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects

(2013) Zhixiu Li et al.   Annual Review of Biophysics

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

(2013) J. Zhang et al.   BIOINFORMATICS

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational modification of protein stability by targeting surface sites leads to complicated results

(2013) S. Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arginine Topology Controls Escape of Minimally Cationic Proteins from Early Endosomes to the Cytoplasm

(2012) Jacob S. Appelbaum et al.   CHEMISTRY & BIOLOGY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis for the Versatile Interactions of Smad7 with Regulator WW Domains in TGF-β Pathways

(2012) Eric Aragón et al.   STRUCTURE

Accelerated NMR Spectroscopy by Using Compressed Sensing

(2011) Krzysztof Kazimierczuk et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Contribution of Hydrophobic Interactions to Protein Stability

(2011) C. Nick Pace et al.   JOURNAL OF MOLECULAR BIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

A novel strategy for NMR resonance assignment and protein structure determination

(2010) Alexander Lemak et al.   JOURNAL OF BIOMOLECULAR NMR

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

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

De Novo Design of a βαβ Motif

(2009) Huanhuan Liang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Analysis of Core Packing in a Cooperatively Folded Miniature Protein: The Ultrafast Folding Villin Headpiece Helical Subdomain

(2009) Shifeng Xiao et al.   BIOCHEMISTRY

The Folding Mechanism of BBL: Plasticity of Transition-State Structure Observed within an Ultrafast Folding Protein Family

(2009) Hannes Neuweiler et al.   JOURNAL OF MOLECULAR BIOLOGY

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Sequence determinants of thermodynamic stability in a WW domain-An all-β-sheet protein

(2009) Marcus Jäger et al.   PROTEIN SCIENCE

Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach

(2008) Alexander Lemak et al.   JOURNAL OF BIOMOLECULAR NMR

Increasing protein stability using a rational approach combining sequence homology and structural alignment: Stabilizing the WW domain

(2002) Xin Jiang et al.   PROTEIN SCIENCE