Essentials of de novo protein design: Methods and applications

Structures and disulfide cross-linking of de novo designed therapeutic mini-proteins

(2018) Daniel-Adriano Silva et al.   FEBS Journal

Accurate computational design of multipass transmembrane proteins

(2018) Peilong Lu et al.   SCIENCE

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

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

Rational design of proteins that exchange on functional timescales

(2017) James A Davey et al.   Nature Chemical Biology

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

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

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures

(2017) Bobo Dang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CCBuilder 2.0: Powerful and accessible coiled-coil modeling

(2017) Christopher W. Wood et al.   PROTEIN SCIENCE

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

Comprehensive computational design of ordered peptide macrocycles

(2017) Parisa Hosseinzadeh 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

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

(2016) Kristoffer E. Johansson et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Computational design of self-assembling cyclic protein homo-oligomers

(2016) Jorge A. Fallas et al.   Nature Chemistry

Installing hydrolytic activity into a completely de novo protein framework

(2016) Antony J. Burton et al.   Nature Chemistry

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

(2016) S. E. Boyken et al.   SCIENCE

Design of structurally distinct proteins using strategies inspired by evolution

(2016) T. M. Jacobs et al.   SCIENCE

Accurate design of megadalton-scale two-component icosahedral protein complexes

(2016) J. B. Bale et al.   SCIENCE

Computationally Designed Bispecific Antibodies using Negative State Repertoires

(2016) Andrew Leaver-Fay et al.   STRUCTURE

A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response

(2016) Merika Treants Koday et al.   PLoS Pathogens

Rational design of α-helical tandem repeat proteins with closed architectures

(2015) Lindsey Doyle et al.   NATURE

Exploring the repeat protein universe through computational protein design

(2015) TJ Brunette et al.   NATURE

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

(2015) Po-Ssu Huang 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

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces

(2015) S. Gonen et al.   SCIENCE

Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships

(2015) Fan Zheng et al.   STRUCTURE

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

(2014) Erik Procko et al.   CELL

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Accurate design of co-assembling multi-component protein nanomaterials

(2014) Neil P. King et al.   NATURE

De novo design of a transmembrane Zn2+-transporting four-helix bundle

(2014) Nathan H. Joh et al.   SCIENCE

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

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Design of Protein Catalysts

(2013) Donald Hilvert   Annual Review of Biochemistry

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

(2013) Christine E. Tinberg et al.   NATURE

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers

(2012) Michael D. Tyka et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Computational design of a protein crystal

(2012) C. J. Lanci 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

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

(2012) Grant S. Murphy et al.   STRUCTURE

Novel proteins: from fold to function

(2011) Betsy A Smith et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

(2011) Po-Ssu Huang et al.   PLoS One

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

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

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

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Probing Designability via a Generalized Model of Helical Bundle Geometry

(2010) Gevorg Grigoryan et al.   JOURNAL OF MOLECULAR BIOLOGY

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

(2010) Michael D. Tyka et al.   JOURNAL OF MOLECULAR BIOLOGY

RosettaHoles2: A volumetric packing measure for protein structure refinement and validation

(2010) William Sheffler et al.   PROTEIN SCIENCE

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction

(2010) J. B. Siegel et al.   SCIENCE

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

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

(2009) Daniel J Mandell et al.   NATURE METHODS

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE