Standout Papers

De novo design of self-assembling helica... 2007 2026 2013 2019 137
  1. De novo design of self-assembling helical protein filaments (2018)
    Hao Shen, Jorge A. Fallas et al. Science
  2. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home (2007)
    Rhiju Das, Bin Qian et al. Proteins Structure Function and Bioinformatics
  3. Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks (2022)
    Shunzhi Wang, William Sheffler et al. Chemistry of Materials
  4. Computational design of mechanically coupled axle-rotor protein assemblies (2022)
    Alexis Courbet, Jesse M. Hansen et al. Science
  5. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site (2017)
    Eva‐Maria Strauch, Steffen M. Bernard et al. Nature Biotechnology
  6. Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS (2018)
    Aniruddha Sahasrabuddhe, Yang Hsia et al. Proceedings of the National Academy of Sciences
  7. Design of multi-scale protein complexes by hierarchical building block fusion (2021)
    Yang Hsia, Rubul Mout et al. Nature Communications
  8. De novo design of a fluorescence-activating β-barrel (2018)
    Jiayi Dou, Anastassia A. Vorobieva et al. Nature
  9. RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation (2008)
    William Sheffler, David Baker Protein Science
  10. Ranking predicted protein structures with support vector regression (2007)
    Jian‐Wen Qiu, William Sheffler et al. Proteins Structure Function and Bioinformatics
  11. Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin (2013)
    Gal Wittenberg, William Sheffler et al. Physical Chemistry Chemical Physics
  12. Computational design of a homotrimeric metalloprotein with a trisbipyridyl core (2016)
    Jeremy H. Mills, William Sheffler et al. Proceedings of the National Academy of Sciences
  13. Accurate design of megadalton-scale two-component icosahedral protein complexes (2016)
    Jacob B. Bale, Shane Gonen et al. Science
  14. Structure prediction for CASP8 with all‐atom refinement using Rosetta (2009)
    Srivatsan Raman, Robert M. Vernon et al. Proteins Structure Function and Bioinformatics
  15. Accurate computational design of multipass transmembrane proteins (2018)
    Peilong Lu, Duyoung Min et al. Science
  16. Design of biologically active binary protein 2D materials (2021)
    Ariel J. Ben‐Sasson, Joseph L. Watson et al. Nature
  17. Multi-input chemical control of protein dimerization for programming graded cellular responses (2019)
    Glenna Foight, Zhizhi Wang et al. Nature Biotechnology
  18. RosettaHoles2: A volumetric packing measure for protein structure refinement and validation (2010)
    William Sheffler, David Baker Protein Science
  19. Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy (2012)
    Neil P. King, William Sheffler et al. Science
  20. Accurate design of co-assembling multi-component protein nanomaterials (2014)
    Neil P. King, Jacob B. Bale et al. Nature
  21. Computational design of self-assembling cyclic protein homo-oligomers (2016)
    Jorge A. Fallas, George Ueda et al. Nature Chemistry
  22. De novo design of pH-responsive self-assembling helical protein filaments (2024)
    Hao Shen, Eric M. Lynch et al. Nature Nanotechnology
  23. Design of a hyperstable 60-subunit protein icosahedron (2016)
    Yang Hsia, Jacob B. Bale et al. Nature
  24. Modeling Disordered Regions in Proteins Using Rosetta (2011)
    Yan Han, William Sheffler et al. PLoS ONE
  25. Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock (2023)
    William Sheffler, Quinton M. Dowling et al. PLoS Computational Biology

Citation Impact

Citing Papers

Principles of assembly reveal a periodic table of protein complexes
2015 Science
An enumerative algorithm for de novo design of proteins with diverse pocket structures
2020 StandoutNobel
Nature of the protein universe
2009 StandoutNobel
Generation of ordered protein assemblies using rigid three-body fusion
2021 StandoutNobel
Principles for designing proteins with cavities formed by curved β sheets
2017 StandoutScienceNobel
Design of structurally distinct proteins using strategies inspired by evolution
2016 Science
Topological control of cytokine receptor signaling induces differential effects in hematopoiesis
2019 StandoutScienceNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
Computational design of closely related proteins that adopt two well-defined but structurally divergent folds
2020 StandoutNobel
Simultaneous prediction of protein folding and docking at high resolution
2009 StandoutNobel
Perturbing the energy landscape for improved packing during computational protein design
2020 StandoutNobel
Hallucinating symmetric protein assemblies
2022 StandoutScienceNobel
Automated de novo prediction of native-like RNA tertiary structures
2007 StandoutNobel
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
2020 StandoutScienceNobel
Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system
2018
Expanding the space of protein geometries by computational design of de novo fold families
2020 Science
Rapid and automated design of two-component protein nanomaterials using ProteinMPNN
2024 StandoutNobel
Sculpting conducting nanopore size and shape through de novo protein design
2024 StandoutScienceNobel
Generative models for graph-based protein design
2019
Four-component protein nanocages designed by programmed symmetry breaking
2024 StandoutNatureNobel
Hierarchical design of pseudosymmetric protein nanocages
2024 StandoutNatureNobel
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4
2015 StandoutNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
A suite of designed protein cages using machine learning and protein fragment-based protocols
2024
Recent advances in de novo protein design: Principles, methods, and applications
2021
De novo design of allosterically switchable protein assemblies
2024 StandoutNatureNobel
Design of symmetric TIM barrel proteins from first principles
2015
Computational Protein Design with Deep Learning Neural Networks
2018
De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
2022
De novo design of immunoglobulin-like domains
2022 StandoutNobel
Two-tier supramolecular encapsulation of small molecules in a protein cage
2020
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
2012
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
2013
The enabled state of DNA nanotechnology
2013
Designing repeat proteins: a modular approach to protein design
2017
Computational Design of a Protein-Based Enzyme Inhibitor
2013 StandoutNobel
Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core
2012
Control of repeat-protein curvature by computational protein design
2015 StandoutNobel
A De Novo Protein Binding Pair By Computational Design and Directed Evolution
2011 StandoutNobel
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
2011 StandoutNobel
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
2024 StandoutNobel
A Double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms
2008 StandoutNobel
A Vast Repertoire of Dscam Binding Specificities Arises from Modular Interactions of Variable Ig Domains
2007 StandoutNobel
A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
2012
Constructing protein polyhedra via orthogonal chemical interactions
2020 Nature
Designed proteins induce the formation of nanocage-containing extracellular vesicles
2016 Nature
Improving de novo protein binder design with deep learning
2023 StandoutNobel
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
High-Resolution Comparative Modeling with RosettaCM
2013 StandoutNobel
Transient water wires mediate selective proton transport in designed channel proteins
2023
Chemical shift-based methods in NMR structure determination
2018
Engineering and functionalization of large circular tandem repeat protein nanoparticles
2020
Opportunities and challenges in design and optimization of protein function
2024
De novo design of luciferases using deep learning
2023 StandoutNatureNobel
Principles for designing ideal protein structures
2012 StandoutNatureNobel
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational
2021
Protein structure prediction: when is it useful?
2009
Protein folding and de novo protein design for biotechnological applications
2013
Structure of a designed protein cage that self-assembles into a highly porous cube
2014
Constructing ion channels from water-soluble α-helical barrels
2021
Low-N protein engineering with data-efficient deep learning
2021
Evolution of a designed protein assembly encapsulating its own RNA genome
2017 StandoutNatureNobel
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
Crystallographic model validation: from diagnosis to healing
2013
The coming of age of de novo protein design
2016 StandoutNatureNobel
Geometrical assembly of ultrastable protein templates for nanomaterials
2016
A backbone-centred energy function of neural networks for protein design
2022 Nature
Bioengineered protein-based nanocage for drug delivery
2016
Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells
2023 StandoutNobel
Designing protein structures and complexes with the molecular modeling program Rosetta
2019
Self-assembling protein nanoparticles in the design of vaccines
2015
Expanding and reprogramming the genetic code
2017 Nature
Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces
2021
The Phenix software for automated determination of macromolecular structures
2011
De novo design of bioactive protein switches
2019 StandoutNatureNobel
Practical approaches to designing novel protein assemblies
2013
Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
2010 StandoutNobel
Gigadalton-scale shape-programmable DNA assemblies
2017 Nature
De novo design of a non-local β-sheet protein with high stability and accuracy
2018 StandoutNobel
De Novo Enzyme Design Using Rosetta3
2011 StandoutNobel
Rationale in Custom Design of Transmembrane β-Barrel Pores
2024
Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks
2017 StandoutNobel
De novo protein design: how do we expand into the universe of possible protein structures?
2015
Programmable design of orthogonal protein heterodimers
2018 StandoutNatureNobel
Controlling protein assembly on inorganic crystals through designed protein interfaces
2019 StandoutNatureNobel
A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold
2019
Protein sequence design with a learned potential
2022
Design and self-assembly of simple coat proteins for artificial viruses
2014
Proteins evolve on the edge of supramolecular self-assembly
2017 Nature
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage
2014 StandoutNobel
A General Computational Approach for Repeat Protein Design
2014 StandoutNobel
Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments
2013
An accurate binding interaction model in de novo computational protein design of interactions: If you build it, they will bind
2013
De novo protein design by deep network hallucination
2021 StandoutNatureNobel
De novo design of a nanopore for single-molecule detection that incorporates a β-hairpin peptide
2021
Exploitation of binding energy for catalysis and design
2009 StandoutNatureNobel
De novo protein design by inversion of the AlphaFold structure prediction network
2023
Computational design of a leucine-rich repeat protein with a predefined geometry
2014
MolProbity: More and better reference data for improved all‐atom structure validation
2017 Standout
Engineering a Rugged Nanoscaffold To Enhance Plug-and-Display Vaccination
2018
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks
2020
De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities
2019
QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities
2018
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity
2024 StandoutNobel
Design and Characterization of an Icosahedral Protein Cage Formed by a Double-Fusion Protein Containing Three Distinct Symmetry Elements
2020
Self-Assembling 2D Arrays with de Novo Protein Building Blocks
2019 StandoutNobel
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
2016 StandoutScienceNobel
Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer
2011
Self-Assembling Cages from Coiled-Coil Peptide Modules
2013 Science
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
2014 StandoutNobel
Protein self-assembly via supramolecular strategies
2016
Symmetry‐Directed Self‐Assembly of a Tetrahedral Protein Cage Mediated by de Novo‐Designed Coiled Coils
2017
Structural DNA Nanotechnology: State of the Art and Future Perspective
2014
Computational design and experimental verification of a symmetric protein homodimer
2015
F‐domain valency determines outcome of signaling through the angiopoietin pathway
2021 StandoutNobel
Computational design of environmental sensors for the potent opioid fentanyl
2017 StandoutNobel
Engineering Biomolecular Self‐Assembly at Solid–Liquid Interfaces
2020 StandoutNobel
De novo protein fold design through sequence-independent fragment assembly simulations
2023
Generalized ensemble methods for de novo structure prediction
2009 StandoutNobel
Macromolecular Modeling with Rosetta
2008 StandoutNobel
Modular repeat protein sculpting using rigid helical junctions
2020 StandoutNobel
Antibody-dependent enhancement of influenza disease promoted by increase in hemagglutinin stem flexibility and virus fusion kinetics
2019
Metal‐dependent assembly of a protein nano‐cage
2019
Design of self-assembling transmembrane helical bundles to elucidate principles required for membrane protein folding and ion transport
2017
Self-Assembling Nano-Architectures Created from a Protein Nano-Building Block Using an Intermolecularly Folded Dimeric de Novo Protein
2015
De novo design of small beta barrel proteins
2023 StandoutNobel
Designing and defining dynamic protein cage nanoassemblies in solution
2016
Self-Assembly of an α-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework
2016
Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein
2019 StandoutNobel
Designed Protein Cages as Scaffolds for Building Multienzyme Materials
2020
Characterization of a highly flexible self‐assembling protein system designed to form nanocages
2013
Control over overall shape and size in de novo designed proteins
2015 StandoutNobel
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
2017 StandoutNobel
Flexible, symmetry-directed approach to assembling protein cages
2016
Essentials of de novo protein design: Methods and applications
2018
Large-scale determination of previously unsolved protein structures using evolutionary information
2015 StandoutNobel
De novo design of protein homodimers containing tunable symmetric protein pockets
2022 StandoutNobel
Structure and Flexibility of Nanoscale Protein Cages Designed by Symmetric Self-Assembly
2013
Surface-Directed Assembly of Sequence-Defined Synthetic Polymers into Networks of Hexagonally Patterned Nanoribbons with Controlled Functionalities
2016
Validation of de novo designed water‐soluble and transmembrane β‐barrels by in silico folding and melting
2024
Top-down design of protein architectures with reinforcement learning
2023 StandoutScienceNobel
Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures
2016
Computational design of a symmetric homodimer using β-strand assembly
2011
Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability
2019
Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site
2023 StandoutNobel
Protein Assembly by Design
2021
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
2010
Reconfigurable asymmetric protein assemblies through implicit negative design
2022 StandoutScienceNobel
A complete rule set for designing symmetry combination materials from protein molecules
2020
Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
2015 StandoutScienceNobel

Works of William Sheffler being referenced

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
2023 StandoutNobel
Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS
2018 StandoutNobel
Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy
2012 StandoutScienceNobel
De novo design of self-assembling helical protein filaments
2018 StandoutScienceNobel
Accurate computational design of multipass transmembrane proteins
2018 StandoutScienceNobel
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
2007 StandoutNobel
Multi-input chemical control of protein dimerization for programming graded cellular responses
2019 StandoutNobel
Accurate design of co-assembling multi-component protein nanomaterials
2014 StandoutNatureNobel
Computational design of self-assembling cyclic protein homo-oligomers
2016 StandoutNobel
Design of biologically active binary protein 2D materials
2021 StandoutNatureNobel
A New Generation of Crystallographic Validation Tools for the Protein Data Bank
2011
Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site
2017 StandoutNobel
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Design of multi-scale protein complexes by hierarchical building block fusion
2021 StandoutNobel
Structure prediction for CASP8 with all‐atom refinement using Rosetta
2009 StandoutNobel
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation
2008 StandoutNobel
RosettaHoles2: A volumetric packing measure for protein structure refinement and validation
2010 StandoutNobel
Accurate design of megadalton-scale two-component icosahedral protein complexes
2016 StandoutScienceNobel
Computational design of a homotrimeric metalloprotein with a trisbipyridyl core
2016 StandoutNobel
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
Design of a hyperstable 60-subunit protein icosahedron
2016 StandoutNatureNobel
Rankless by CCL
2026