Top-down design of protein architectures with reinforcement learning

De novo protein fold design through sequence-independent fragment assembly simulations

(2023) Robin Pearce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design of protein-binding proteins from the target structure alone

(2022) Longxing Cao et al.   NATURE

Scaffolding protein functional sites using deep learning

(2022) Jue Wang et al.   SCIENCE

Discovering faster matrix multiplication algorithms with reinforcement learning

(2022) Alhussein Fawzi et al.   NATURE

Hallucinating symmetric protein assemblies

(2022) B. I. M. Wicky et al.   SCIENCE

Robust deep learning–based protein sequence design using ProteinMPNN

(2022) J. Dauparas et al.   SCIENCE

Design of biologically active binary protein 2D materials

(2021) Ariel J. Ben-Sasson et al.   NATURE

Practical considerations for using K3 cameras in CDS mode for high-resolution and high-throughput single particle cryo-EM

(2021) Ming Sun et al.   JOURNAL OF STRUCTURAL BIOLOGY

Adjuvanting a subunit COVID-19 vaccine to induce protective immunity

(2021) Prabhu S. Arunachalam et al.   NATURE

Quadrivalent influenza nanoparticle vaccines induce broad protection

(2021) Seyhan Boyoglu-Barnum et al.   NATURE

Designed proteins assemble antibodies into modular nanocages

(2021) Robby Divine et al.   SCIENCE

Design of multi-scale protein complexes by hierarchical building block fusion

(2021) Yang Hsia et al.   Nature Communications

Protein Assembly by Design

(2021) Jie Zhu et al.   CHEMICAL REVIEWS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

F‐domain valency determines outcome of signaling through the angiopoietin pathway

(2021) Yan Ting Zhao et al.   EMBO REPORTS

Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces

(2021) Jazmine P. Hallinan et al.   Communications Biology

Deep Reinforcement Learning for Autonomous Driving: A Survey

(2021) B Ravi Kiran et al.   IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens

(2020) George Ueda et al.   eLife

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

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

(2017) Gabriel J. Rocklin et al.   SCIENCE

Opposing actions of angiopoietin-2 on Tie2 signaling and FOXO1 activation

(2016) Minah Kim et al.   JOURNAL OF CLINICAL INVESTIGATION

Design of a hyperstable 60-subunit protein icosahedron

(2016) Yang Hsia et al.   NATURE

Designed proteins induce the formation of nanocage-containing extracellular vesicles

(2016) Jörg Votteler et al.   NATURE

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Computational design of self-assembling cyclic protein homo-oligomers

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

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

Amelioration of sepsis by TIE2 activation–induced vascular protection

(2016) Sangyeul Han et al.   Science Translational Medicine

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

(2016) Ray Yu-Ruei Wang et al.   eLife

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

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

(2015) S. Gonen et al.   SCIENCE

Flow Cytometry Reveals that H5N1 Vaccination Elicits Cross-Reactive Stem-Directed Antibodies from Multiple Ig Heavy-Chain Lineages

(2014) J. R. R. Whittle et al.   JOURNAL OF VIROLOGY

Accurate design of co-assembling multi-component protein nanomaterials

(2014) Neil P. King et al.   NATURE

Structure of a designed protein cage that self-assembles into a highly porous cube

(2014) Yen-Ting Lai et al.   Nature Chemistry

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

(2013) Lucas Gregorio Nivón et al.   PLoS One

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin

(2012) B. Zakeri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

Structure of a 16-nm Cage Designed by Using Protein Oligomers

(2012) Y.-T. Lai et al.   SCIENCE

Highly Conserved Protective Epitopes on Influenza B Viruses

(2012) C. Dreyfus et al.   SCIENCE

Protein design with fragment databases

(2011) Erik Verschueren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Broadly Neutralizing Human Monoclonal Antibody That Recognizes a Conserved, Novel Epitope on the Globular Head of the Influenza H1N1 Virus Hemagglutinin

(2011) J. C. Krause et al.   JOURNAL OF VIROLOGY

Generation of protein lattices by fusing proteins with matching rotational symmetry

(2011) John C. Sinclair et al.   Nature Nanotechnology

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

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

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

(2011) Dominik Gront et al.   PLoS One

Features and development ofCoot

(2010) P. Emsley 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