Machine learning enhanced atom probe tomography analysis

Y. Li; Y. Wei; A. Saxena; M. Kühbach; C. Freysoldt et al. 

Accurate single-domain scaffolding of three nonoverlapping protein epitopes using deep learning

K. M. Castro; J. Wang; S. Georgeon; B. E. Correia 

Mapping the latent CRBN-molecular glue degrader interactome

P. Galli; S. Xiao; Y. Meng; A. Hanzl; A. M. Bendel et al. 

Leveraging protein representations to explore uncharted fold spaces with generative models

B. Correia; Y. Miao; M. Pacesa; S. Georgeon; J. Schmidt et al. 

Probing the energy landscape of α-Synuclein amyloid fibril formation by systematic K-to-Q mutagenesis

A. Kunka; A. Farzadfard; J. A. Larsen; F. Saraceno; R. K. Norrild et al. 

Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity

K. M. Castro Gilabert; R. Ayardulabi; S. Wehrle; H. Cui; S. Georgeon et al. 

Structures of a synthetic antibody selected against and bound to the C‐terminal domain of Clostridium perfringens enterotoxin

C. P. Ogbu; N. Goldbach; M. Pačesa; S. Kapoor; B. E. Correia et al. 

De novo design of phosphorylation-induced protein switches for synthetic signaling in cells

S. Buckley; Y. Miao; M. Idris; P. Lee; L. Scheller et al. 

Applications and properties of computationally designed de novo proteins

M. Pacesa 

One-shot Design of Functional Protein Binders with Bindcraft

M. Pacesa; L. Nickel; C. Schellhaas; J. Schmidt; E. Pyatova et al. 

Design of Highly Functional Genome Editors by Modelling Crispr-cas Sequences

J. Ruffolo; S. Nayfach; J. Gallagher; A. Bhatnagar; J. Beazer et al. 

Probing the Effect of the Disordered Flank Regions on Amyloid Fibril Growth and Proliferation

J. Aunstrup Larsen; J. H. M. van Gils; S. Ray; M. Dickmanns; S. Wang et al. 

Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning

R. A. Silverstein; N. Kim; A-S. Kroell; R. T. Walton; J. Delano et al. 

Computationally designed stem-epitope mimetics elicit broadly reactive antibodies

S. Wehrle; A. Scheck; L. Reusch; F. L. Matassoli; S. Georgeon et al. 

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

A. Marchand; S. Buckley; A. Schneuing; M. Pacesa; M. Elia et al. 

Towards Conformational Targeting of Alpha-Synuclein Fibrils

Boosting Protein Graph Representations through Static-Dynamic Fusion

P. Guo; B. Ferreira de Sousa Correia; P. Vandergheynst; D. Probst 

Computational design of complex protein folds and soluble analogs of membrane proteins

Computational Design of Protein Switches

The physiological landscape and specificity of antibody repertoires are consolidated by multiple immunizations

L. Csepregi; K. Hoehn; D. Neumeier; J. M. Taft; S. Friedensohn et al. 

A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins

T. Stadelmann; D. Heid; M. Jendrusch; J. Mathony; S. Aschenbrenner et al. 

Structure-based drug design with equivariant diffusion models

A. Schneuing; C. Harris; Y. Du; K. Didi; A. Jamasb et al. 

Epitope-focused immunogens targeting the hepatitis C virus glycoproteins induce broadly neutralizing antibodies

K. Nagarathinam; A. Scheck; M. Labuhn; L. J. Stroeh; E. Herold et al. 

Machine Learning-Enabled Tomographic Imaging of Chemical Short-Range Atomic Ordering

Y. Li; T. Colnaghi; Y. Gong; H. Zhang; Y. Yu et al. 

FSscore: A Personalized Machine Learning-Based Synthetic Feasibility Score

R. M. Neeser; B. Correia; P. Schwaller 

Dual ON/OFF-switch chimeric antigen receptor controlled by two clinically approved drugs

G. M. P. G. Attianesea; S. Shui; E. Cribioli; M. Triboulet; L. Scheller et al. 

Exploring “dark-matter” protein folds using deep learning

Z. Harteveld; A. Van Hall-Beauvais; I. Morozova; J. Southern; C. Goverde et al. 

Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses

I. Fernández; F. Bontems; D. Brun; Y. Coquin; C. Goverde et al. 

An evolved artificial radical cyclase enables the construction of bicyclic terpenoid scaffolds via an H-atom transfer pathway

D. Chen; X. Zhang; A. A. Vorobieva; R. Tachibana; A. Stein et al. 

3D deep learning for enhanced atom probe tomography analysis of nanoscale microstructures

J. Yu; Z. Wang; A. Saksena; S. Wei; Y. Wei et al. 

Roadmap on data-centric materials science

S. Bauer; P. Benner; T. Bereau; V. Blum; M. Boley et al. 

Computational design of soluble and functional membrane protein analogues

C. A. Goverde; M. Pacesa; N. Goldbach; L. J. Dornfeld; P. E. Balbi et al. 

Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation

Z. M. Xu; G. E. Gnouamozi; S. Rueger; P. R. Shea; M. Buti et al. 

Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins

A. S. Petruzzella; M. Bruand; A. Santamaria-Martinez; N. Katanayeva; L. Reymond et al. 

Opportunities and challenges in design and optimization of protein function

D. Listov; C. A. Goverde; B. E. Correia; S. J. Fleishman 

Equivariant 3D-conditional diffusion model for molecular linker design

I. Igashov; H. Stärk; C. Vignac; A. Schneuing; V. G. Satorras et al. 

A Synthetic Multivalent Lipopeptide Derived from Pam3CSK4 with Irreversible Influenza Inhibition and Immuno-Stimulating Effects

Y. Zhu; L. Wei; A. C-A. Zwygart; P. Gainza; Q. O. Khac et al. 

Past, present, and future of CRISPR genome editing technologies

M. Pacesa; O. Pelea; M. Jinek 

An atlas of protein homo-oligomerization across domains of life

H. Schweke; M. Pacesa; T. Levin; C. A. Goverde; P. Kumar et al. 

Multi-motif scaffolding for de novo pathogen antigen mimetics by deep generative learning

Predicting protein interactions using geometric deep learning on protein surfaces

Chemically disruptable molecule switch and use thereof

P. Gainza Cirauqui; B. E. Correia; L. Tang; A. Marchand; L. Bonati et al. 

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

A PD-L1/EGFR bispecific antibody combines immune checkpoint blockade and direct anti-cancer action for an enhanced anti-tumor response

L. Rubio-Perez; R. Lazaro-Gorines; S. L. Harwood; M. Compte; R. Navarro et al. 

A new age in protein design empowered by deep learning

H. Khakzad; I. Igashov; A. Schneuing; C. Goverde; M. Bronstein et al. 

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

S. Shui; L. Scheller; B. E. Correia 

Deformation response of highly stretchable and ductile graphene kirigami under uniaxial and biaxial tension

P. Shi; Y. Chen; Y. Wei; J. Feng; T. Guo et al. 

Rational design of small-molecule responsive protein switches

S. Shui; S. Buckley; L. Scheller; B. E. Correia 

Rules and mechanisms governing G protein coupling selectivity of GPCRs

I. Masuho; R. Kise; P. Gainza; E. Von Moo; X. Li et al. 

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

H. Schweke; Q. Xu; G. Tauriello; L. Pantolini; T. Schwede et al. 

Rational Design of Chemically Controlled Antibodies and Protein Therapeutics

A. Marchand; L. Bonati; S. Shui; L. Scheller; P. Gainza Cirauqui et al. 

De novo protein design by inversion of the AlphaFold structure prediction network

C. Goverde; B. Wolf; H. Khakzad; S. Rosset; B. Correia 

New protein–protein interactions designed by a computer

A. Marchand; P. Gainza Cirauqui 

De novo design of protein interactions with learned surface fingerprints

P. Gainza Cirauqui; S. Wehrle; A. K. Van Hall-Beauvais; A. Marchand; A. Scheck et al. 

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

C. Gueto-Tettay; D. Tang; L. Happonen; M. Heusel; H. Khakzad et al. 

Track: Machine Learning in Protein Science De Novo Design of Viral Epitope Mimetics with Non-Regular Structural Features

K. Castro; J. Wang; L. Milles; J. Watson; R. Ragotte et al. 

De novo designed proteins: a study in engineering novel folds and functions

Computational design of vaccine immunogens

K. M. Castro; A. Scheck; S. Xiao; B. E. Correia 

Invasive Streptococcal Infection Can Lead to the Generation of Cross-Strain Opsonic Antibodies

T. de Neergaard; A. Blaeckberg; H. Ivarsson; S. Thomasson; V. K. Ahnlide et al. 

A generic framework for hierarchical de novo protein design

Z. Harteveld; J. Bonet; S. Rosset; C. Yang; F. Sesterhenn et al. 

Assessing and enhancing foldability in designed proteins

D. Listov; R. Lipsh-Sokolik; S. Rosset; C. Yang; B. E. Correia et al. 

Programmable DARPin-based receptors for the detection of thrombotic markers

T. Strittmatter; Y. Wang; A. Bertschi; L. Scheller; P. C. Freitag et al. 

Antibodies to combat viral infections: development strategies and progress

G. Pantaleo; B. Correia; C. Fenwick; V. S. Joo; L. Perez 

Computational design of novel protein–protein interactions – An overview on methodological approaches and applications

A. Marchand; A. K. Van Hall-Beauvais; B. Correia 

Rational design of protein switches: applications in synthetic biology and cancer immunotherapy

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Novel chemically controlled cellular switches

B. E. Correia; S. Shui; P. Gainza Cirauqui 

A method and system for fast end-to-end learning on protein surfaces

M. Bronstein; F. Sverrisson; J. Pierre Feydy; P. Gainza; B. Ferreira De Sousa Correia 

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Computational design of bioactive protein switches with multi-logics for cell-based therapeutics

S. Shui; P. Gainza; L. Scheller; C. Yang; B. Correia 

De Novo Design of Site-specific Protein Binders Using Surface Fingerprints

S. Wehrle; A. Van Hall-Beauvais; P. Gainza; Z. Harteveld; A. Scheck et al. 

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

B. Anton; M. Besalu; O. Fornes; J. Bonet; A. Molina et al. 

A Nanoscaffolded Spike-RBD Vaccine Provides Protection against SARS-CoV-2 with Minimal Anti-Scaffold Response

D. Lainšček; T. Fink; V. Forstnerič; I. Hafner-Bratkovič; S. Orehek et al. 

Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning

D. M. Mason; S. Friedensohn; C. R. Weber; C. Jordi; B. Wagner et al. 

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

C. T. Schoeder; S. Schmitz; J. Adolf-Bryfogle; A. M. Sevy; J. A. Finn et al. 

Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein

M. D. Hoffmann; J. Mathony; J. U. Zu Belzen; Z. Harteveld; S. Aschenbrenner et al. 

A Rosetta-based protein design protocol converging to natural sequences

G. Sormani; Z. Harteveld; S. Rosset; B. Correia; A. Laio 

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

J. Aguirre-Plans; A. Meseguer; R. Molina-Fernandez; M. A. Marin-Lopez; G. Jumde et al. 

Bottom-up de novo design of functional proteins with complex structural features

C. Yang; F. Sesterhenn; J. Bonet; E. A. van Aalen; L. Scheller et al. 

On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C

Preclinical development of a humanized chimeric antigen receptor against B-cell maturation antigen for multiple myeloma

L. Perez-Amill; G. Sune; A. Antonana-Vildosola; M. Castella; A. Najjar et al. 

Fast end-to-end learning on protein surfaces

F. Sverrisson; J. Feydy; B. E. Correia; M. M. Bronstein 

Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity

A. Frangolho; B. Correia; D. C. Vaz; Z. L. Almeida; R. M. M. Brito 

Designs and Characterization of Subunit Ebola GP Vaccine Candidates: Implications for Immunogenicity

V. Agnolon; D. Kiseljak; M. J. Wurm; F. M. Wurm; C. Foissard et al. 

Picometer Resolution Structure of the Coordination Sphere in the Metal-Binding Site in a Metalloprotein by NMR

A. Bertarello; L. Benda; K. J. Sanders; A. J. Pell; M. J. Knight et al. 

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

A. Meseguer; F. Arman; O. Fornes; R. Molina-Fernandez; J. Bonet et al. 

Macromolecular modeling and design in Rosetta: recent methods and frameworks

J. K. Leman; B. D. Weitzner; S. M. Lewis; J. Adolf-Bryfogle; N. Alam et al. 

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

F. Sesterhenn; C. Yang; J. Bonet; J. T. Cramer; X. Wen et al. 

Computational design of anti-CRISPR proteins with improved inhibition potency

J. Mathony; Z. Harteveld; C. Schmelas; J. U. zu Belzen; S. Aschenbrenner et al. 

Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth

S. Moussu; C. Broyart; G. Santos-Fernandez; S. Augustin; S. Wehrle et al. 

Epitope Mapping and Fine Specificity of Human T and B Cell Responses for Novel Candidate Blood-Stage Malaria Vaccine P27A

K. M. Geiger; D. Guignard; C. Yang; J-P. Bikorimana; B. E. Correia et al. 

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

G. Giordano-Attianese; P. Gainza; E. Gray-Gaillard; E. Cribioli; S. Shui et al. 

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

M. J. C. Long; A. Van Hall-Beauvais; Y. Aye 

Immunogen

B. Correia; F. Sesterhenn 

Immunogen

B. Correia; F. Sesterhenn; C. Yang; J. Bonet 

Functional de novo Protein Design for Targeted Vaccines and Synthetic Biology Applications

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

P. Gainza; F. Sverrisson; F. Monti; E. Rodolà; D. Boscaini et al. 

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-alpha 7 mediated nuclear import pathway

P. Resa-Infante; J. Bonet; S. Thiele; M. Alawi; S. Stanelle-Bertram et al. 

Decrypting interaction fingerprints in protein molecular surfaces

P. Gainza; F. Sverrisson; F. Monti; M. Bronstein; B. Correia 

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

J. Bonet; Z. Harteveld; F. Sesterhenn; A. Scheck; B. E. Correia 

Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9

F. Bubeck; M. D. Hoffmann; Z. Harteveld; S. Aschenbrenner; A. Bietz et al. 

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

J. Munro; F. Sesterhenn; M. Galloux; S. S. Vollers; L. Csepregi et al. 

Heterodimeric inactivatable chimeric antigen receptors

G. Coukos; M. Irving; B. Correia; P. Gainza-Cirauqui; G. Giordano Attianese 

Expanding beyond the natural protein repertoire to engineer targeted vaccines and diagnostics

Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9

F. Bubeck; M. D. Hoffmann; Z. Harteveld; S. Aschenbrenner; A. Bietz et al. 

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

J. Bonet; S. Wehrle; K. Schriever; C. Yang; A. Billet et al. 

Driving Immune Responses with Synthetic Proteins – Development of De Novo Designed Immunogens to Elicit Respiratory Syncytial Virus Neutralizing Antibodies

F. Sesterhenn; C. Yang; J. Bonet; M. Galloux; X. Wen et al. 

Design and characterization of near-native Ebola GP vaccine candidates: implications for immunogenicity

V. Agnolon; I. Ayadi; J. P. Bikorimana; D. Kiseljak; V. De Vaux et al. 

Expanding the druggable proteome: Ligand and target discovery by fragment-based screening in cells

C. Parker; A. Galmozzi; Y. Wang; B. Correia; E. Saez et al. 

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

F. Sesterhenn; J. Bonet; B. E. Correia 

OFF-switch CAR T cell for safety-enhanced cancer immunotherapy

E. F. Gray-Gaillard; G. G. Attianese; P. Gainza-Cirauqui; S. Vollers; S. Shui et al. 

Computational protein design – the next generation tool to expand synthetic biology applications

P. Gainza-Cirauqui; B. Correia 

ATTACK, a novel bispecific T cell-recruiting antibody with trivalent EGFR binding and monovalent CD3 binding for cancer immunotherapy

S. Harwood; A. Alvarez-Cienfuegos; N. Nunez-Prado; M. Compte; S. Hernandez-Perez et al. 

Bispecific light T-cell engagers for gene-based immunotherapy of epidermal growth factor receptor (EGFR)-positive malignancies

K. Molgaard; S. Harwood; M. Compte; N. Merino; J. Bonet et al. 

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures

M. Marin-Lopez; J. Planas-Iglesias; J. Aguirre-Plans; J. Bonet; J. Garcia-Garcia et al. 

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research

D. Poglayen; M. Alejandro Marin-Lopez; J. Bonet; O. Fornes; J. Garcia-Garcia et al. 

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

E. Sarti; I. Gladich; S. Zamuner; B. E. Correia; A. Laio 

Proof of principle for epitope-focused vaccine design

B. Correia; J. Bates; R. Loomis; C. Carrico; J. Jardine et al. 

Understanding protein recognition using structural features

M. A. Marin-Lopez; J. Planas-Iglesias; J. Bonet; D. Poglayen; J. Garcia-Garcia et al.