Computational design of a modular protein sense-response system

Strategies for designing non-natural enzymes and binders

(2018) Horst Lechner et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

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

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

Modular engineering of cellular signaling proteins and networks

(2016) Russell M Gordley et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Atomic resolution structure of a chimeric DNA–RNA Z-type duplex in complex with Ba2+ions: a case of complicated multi-domain twinning

(2016) Miroslaw Gilski et al.   Acta Crystallographica Section D-Structural Biology

NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells

(2015) Andrew S. Dixon et al.   ACS Chemical Biology

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

(2015) Po-Ssu Huang et al.   Nature Chemical Biology

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

(2015) Noah Ollikainen et al.   PLoS Computational Biology

A general strategy to construct small molecule biosensors in eukaryotes

(2015) Justin Feng et al.   eLife

Computational design of water-soluble α-helical barrels

(2014) Andrew R. Thomson et al.   SCIENCE

High thermodynamic stability of parametrically designed helical bundles

(2014) Po-Ssu Huang et al.   SCIENCE

Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

(2014) Christian X. Weichenberger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2013) Christine E. Tinberg et al.   NATURE

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles

(2013) James A. Davey et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

(2013) Zachary Z. Sun et al.   Jove-Journal of Visualized Experiments

Towards automated crystallographic structure refinement withphenix.refine

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

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation

(2012) M. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multistate approaches in computational protein design

(2012) James A. Davey et al.   PROTEIN SCIENCE

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

Dimerization-Dependent Green and Yellow Fluorescent Proteins

(2012) Spencer C. Alford et al.   ACS Synthetic Biology

Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface

(2011) Mariana Babor et al.   PROTEIN SCIENCE

Biosensors and their applications in microbial metabolic engineering

(2011) Fuzhong Zhang et al.   TRENDS IN MICROBIOLOGY

Structural Basis of Response Regulator Inhibition by a Bacterial Anti-Activator Protein

(2011) Melinda D. Baker et al.   PLOS BIOLOGY

Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRζ fragments

(2010) Walter M. Kim et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

XDS

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

Features and development ofCoot

(2010) P. Emsley et al.   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

Structural Determinants for Improved Stability of Designed Ankyrin Repeat Proteins with a Redesigned C-Capping Module

(2010) Michaela A. Kramer et al.   JOURNAL OF MOLECULAR BIOLOGY

Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase

(2009) Simon Jenni et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

electronic Ligand Builder and Optimization Workbench(eLBOW): a tool for ligand coordinate and restraint generation

(2009) Nigel W. Moriarty et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

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

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design

(2008) Elisabeth L. Humphris et al.   STRUCTURE