Design of protein-binding proteins from the target structure alone

De novo design of modular and tunable protein biosensors

(2021) Alfredo Quijano-Rubio et al.   NATURE

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds

(2021) Brian Coventry et al.   PLoS Computational Biology

Designed proteins assemble antibodies into modular nanocages

(2021) Robby Divine et al.   SCIENCE

Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease

(2021) James Brett Case et al.   Cell Host & Microbe

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Modular repeat protein sculpting using rigid helical junctions

(2020) TJ Brunette et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulation of Signaling Mediated by TSLP and IL-7 in Inflammation, Autoimmune Diseases, and Cancer

(2020) Iva Marković et al.   Frontiers in Immunology

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

(2020) Longxing Cao et al.   SCIENCE

Perturbing the energy landscape for improved packing during computational protein design

(2020) Jack B. Maguire et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2019) Daniel-Adriano Silva et al.   NATURE

A small-molecule fusion inhibitor of influenza virus is orally active in mice

(2019) Maria J. P. van Dongen et al.   SCIENCE

The PSIPRED Protein Analysis Workbench: 20 years on

(2019) Daniel W A Buchan et al.   NUCLEIC ACIDS RESEARCH

The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years

(2019) Marek Grabowski et al.   Structural Dynamics-US

How ligand binds to the type 1 insulin-like growth factor receptor

(2018) Yibin Xu et al.   Nature Communications

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

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

Principles for computational design of binding antibodies

(2017) Dror Baran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Potent peptidic fusion inhibitors of influenza virus

(2017) Rameshwar U. Kadam et al.   SCIENCE

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

(2017) Gabriel J. Rocklin et al.   SCIENCE

Structure and antagonism of the receptor complex mediated by human TSLP in allergy and asthma

(2017) Kenneth Verstraete et al.   Nature Communications

Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses

(2016) M. Gordon Joyce et al.   CELL

Tertiary alphabet for the observable protein structural universe

(2016) Craig O. Mackenzie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain

(2016) Tristan I. Croll et al.   STRUCTURE

GC1118, an Anti-EGFR Antibody with a Distinct Binding Epitope and Superior Inhibitory Activity against High-Affinity EGFR Ligands

(2015) Y. Lim et al.   MOLECULAR CANCER THERAPEUTICS

Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems

(2015) Joseph J. Gillespie et al.   mBio

A neutron-diffraction study of the low-cycle fatigue behaviour of an austenitic stainless steel 316

(2015) Adelaide Dubreuil et al.   ACTA CRYSTALLOGRAPHICA SECTION A

New tools for structure refinement inPHENIX

(2015) Paul Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION A

The recognition of endocytic signal sequences by the AP2 complex

(2015) P. Evans et al.   ACTA CRYSTALLOGRAPHICA SECTION A

ThePDB_REDOserver for macromolecular structure model optimization

(2014) Robbie P. Joosten et al.   IUCrJ

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

(2013) J. Zhang et al.   BIOINFORMATICS

Addressing polyspecificity of antibodies selected from an in vitro yeast presentation system: a FACS-based, high-throughput selection and analytical tool

(2013) Y. Xu et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Collaboration gets the most out of software

(2013) Andrew Morin et al.   eLife

Refining structures against reflection rank: an alternative metric for electron crystallography

(2012) Alexander S. Eggeman et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Graphical tools for macromolecular crystallography inPHENIX

(2012) Nathaniel Echols et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Cross-neutralization of influenza A viruses mediated by a single antibody loop

(2012) Damian C. Ekiert et al.   NATURE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Linking Crystallographic Model and Data Quality

(2012) P. A. Karplus et al.   SCIENCE

Developability Index: A Rapid In Silico Tool for the Screening of Antibody Aggregation Propensity

(2011) Timothy M. Lauer et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

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

Excited-state molecular structures captured by X-ray transient absorption spectroscopy: a decade and beyond

(2010) Lin X. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION A

Dynamical structural science

(2010) E. Collet   ACTA CRYSTALLOGRAPHICA SECTION A

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Ternary Complex of Transforming Growth Factor-β1 Reveals Isoform-specific Ligand Recognition and Receptor Recruitment in the Superfamily

(2010) Sergei Radaev et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structures of a platelet-derived growth factor/propeptide complex and a platelet-derived growth factor/receptor complex

(2010) A. Hye-Ryong Shim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Acute Lymphoblastic Leukemia-associated JAK1 Mutants Activate the Janus Kinase/STAT Pathway via Interleukin-9 Receptor α Homodimers

(2009) Tekla Hornakova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antibody Recognition of a Highly Conserved Influenza Virus Epitope

(2009) D. C. Ekiert et al.   SCIENCE

Structural and Biophysical Studies of the Human IL-7/IL-7Rα Complex

(2009) Craig A. McElroy et al.   STRUCTURE

The Intrinsic Contributions of Tyrosine, Serine, Glycine and Arginine to the Affinity and Specificity of Antibodies

(2008) Sara Birtalan et al.   JOURNAL OF MOLECULAR BIOLOGY