De novo protein design enables the precise induction of RSV-neutralizing antibodies

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

(2019) Fabian Sesterhenn et al.   PLOS BIOLOGY

Packing of apolar side chains enables accurate design of highly stable membrane proteins

(2019) Marco Mravic et al.   SCIENCE

Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus

(2019) Jessica Marcandalli et al.   CELL

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

(2019) Jaume Bonet et al.   BMC BIOINFORMATICS

A proof of concept for structure-based vaccine design targeting RSV in humans

(2019) Michelle C. Crank et al.   SCIENCE

Towards functional de novo designed proteins

(2019) William M Dawson et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Structure-based immunogen design — leading the way to the new age of precision vaccines

(2018) Fabian Sesterhenn et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1

(2018) Kai Xu et al.   NATURE MEDICINE

Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins

(2018) Jarrod J. Mousa et al.   PLoS Pathogens

Recent progress in broadly neutralizing antibodies to HIV

(2018) Devin Sok et al.   NATURE IMMUNOLOGY

Rosetta FunFolDes – A general framework for the computational design of functional proteins

(2018) Jaume Bonet et al.   PLoS Computational Biology

HIV-1 Cross-Reactive Primary Virus Neutralizing Antibody Response Elicited by Immunization in Nonhuman Primates

(2017) Yimeng Wang et al.   JOURNAL OF VIROLOGY

Massively parallel de novo protein design for targeted therapeutics

(2017) Aaron Chevalier et al.   NATURE

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

(2017) Eva-Maria Strauch et al.   NATURE BIOTECHNOLOGY

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Principles for designing proteins with cavities formed by curved β sheets

(2017) Enrique Marcos et al.   SCIENCE

What Are the Most Powerful Immunogen Design Vaccine Strategies?

(2017) Dennis R. Burton   Cold Spring Harbor Perspectives in Biology

Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein

(2017) Daiyin Tian et al.   Nature Communications

Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies

(2016) Bryan Briney et al.   CELL

Heads, stalks and everything else: how can antibodies eradicate influenza as a human disease?

(2016) Karlynn E Neu et al.   CURRENT OPINION IN IMMUNOLOGY

Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design

(2016) Rino Rappuoli et al.   JOURNAL OF EXPERIMENTAL MEDICINE

High-Resolution Longitudinal Study of HIV-1 Env Vaccine–Elicited B Cell Responses to the Virus Primary Receptor Binding Site Reveals Affinity Maturation and Clonal Persistence

(2016) Yimeng Wang et al.   JOURNAL OF IMMUNOLOGY

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy

(2016) J.M. de la Rosa-Trevín et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural basis of potent Zika–dengue virus antibody cross-neutralization

(2016) Giovanna Barba-Spaeth et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

Dengue virus sero-cross-reactivity drives antibody-dependent enhancement of infection with zika virus

(2016) Wanwisa Dejnirattisai et al.   NATURE IMMUNOLOGY

Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV

(2016) M Gordon Joyce et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen

(2016) J. G. Jardine et al.   SCIENCE

Envelope-specific B-cell populations in African green monkeys chronically infected with simian immunodeficiency virus

(2016) Ruijun Zhang et al.   Nature Communications

Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV

(2016) M Gordon Joyce et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Engineering, Structure and Immunogenicity of the Human Metapneumovirus F Protein in the Postfusion Conformation

(2016) Vicente Más et al.   PLoS Pathogens

De novo protein design: how do we expand into the universe of possible protein structures?

(2015) Derek N Woolfson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

Prefusion F–specific antibodies determine the magnitude of RSV neutralizing activity in human sera

(2015) Joan O. Ngwuta et al.   Science Translational Medicine

Immune history profoundly affects broadly protective B cell responses to influenza

(2015) Sarah F. Andrews et al.   Science Translational Medicine

Anatomy of β-Strands at Protein–Protein Interfaces

(2014) Andrew M. Watkins et al.   ACS Chemical Biology

Frag’r’Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

(2014) Jaume Bonet et al.   BIOINFORMATICS

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

Rapid search for tertiary fragments reveals protein sequence-structure relationships

(2014) Jianfu Zhou et al.   PROTEIN SCIENCE

Molecular Signatures of Hemagglutinin Stem-Directed Heterosubtypic Human Neutralizing Antibodies against Influenza A Viruses

(2014) Yuval Avnir et al.   PLoS Pathogens

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

(2013) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Cross-neutralization of four paramyxoviruses by a human monoclonal antibody

(2013) Davide Corti et al.   NATURE

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Structure of RSV Fusion Glycoprotein Trimer Bound to a Prefusion-Specific Neutralizing Antibody

(2013) J. S. McLellan et al.   SCIENCE

Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus

(2013) J. S. McLellan et al.   SCIENCE

Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space

(2012) Daniel Gottstein et al.   JOURNAL OF BIOMOLECULAR NMR

Isolation of antibody V(D)J sequences from single cell sorted rhesus macaque B cells

(2012) Christopher Sundling et al.   JOURNAL OF IMMUNOLOGICAL METHODS

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Structural and genetic basis for development of broadly neutralizing influenza antibodies

(2012) Daniel Lingwood et al.   NATURE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120

(2012) Anthony P. West et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

(2011) Gemma L. Holliday et al.   FEBS Journal

Design and Characterization of Epitope-Scaffold Immunogens That Present the Motavizumab Epitope from Respiratory Syncytial Virus

(2011) Jason S. McLellan et al.   JOURNAL OF MOLECULAR BIOLOGY

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

(2011) M. L. Azoitei et al.   SCIENCE

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

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

A Neutralizing Antibody Selected from Plasma Cells That Binds to Group 1 and Group 2 Influenza A Hemagglutinins

(2011) D. Corti et al.   SCIENCE

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

Structure of a Major Antigenic Site on the Respiratory Syncytial Virus Fusion Glycoprotein in Complex with Neutralizing Antibody 101F

(2010) J. S. McLellan et al.   JOURNAL OF VIROLOGY

Elicitation of structure-specific antibodies by epitope scaffolds

(2010) G. Ofek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope

(2010) Bruno E. Correia et al.   STRUCTURE

Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning

(2007) Thomas Tiller et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Computational characterization of B-cell epitopes

(2007) Nimrod D. Rubinstein et al.   MOLECULAR IMMUNOLOGY