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

Current opinion in structural biology, 2022-06, Vol.74, p.102370-102370, Article 102370

2022

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Ligand and Target Discovery by Fragment-Based Screening in Human Cells

Cell, 2017-01, Vol.168 (3), p.527-541.e29

2017

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RosettaSurf-A surface-centric computational design approach

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009178-e1009178

2022

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A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells

Cell, 2015-06, Vol.161 (7), p.1668-1680

2015

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Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells

Journal of the American Chemical Society, 2014-07, Vol.136 (30), p.10777-10782

2014

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A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

Cell, 2014-06, Vol.157 (7), p.1644-1656

2014

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Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

Nature (London), 2011-09, Vol.477 (7362), p.111-114

2011

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

Nucleic acids research, 2021-03, Vol.49 (5), p.e29

2021

Volltextzugriff (PDF)

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

Nature biomedical engineering, 2021-06, Vol.5 (6), p.600

2021

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

BMC bioinformatics, 2019-05, Vol.20 (1), p.240-240, Article 240

2019

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Chemoproteomic profiling and discovery of protein electrophiles in human cells

Nature chemistry, 2017-03, Vol.9 (3), p.234

2017

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

Science (American Association for the Advancement of Science), 2011-10, Vol.334 (6054), p.373-376

2011

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Rules and mechanisms governing G protein coupling selectivity of GPCRs

Cell reports (Cambridge), 2023-10, Vol.42 (10), p.113173-113173, Article 113173

2023

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

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006623-e1006623

2018

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A rational blueprint for the design of chemically-controlled protein switches

Nature communications, 2021-10, Vol.12 (1), p.1-12, Article 5754

2021

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Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity

Molecules (Basel, Switzerland), 2020-12, Vol.25 (23), p.5698

2020

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

PLoS biology, 2019-02, Vol.17 (2), p.e3000164-e3000164

2019

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

Structure (London), 2010-09, Vol.18 (9), p.1116-1126

2010

Volltextzugriff (PDF)

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

Nucleic acids research, 2016-04, Vol.44 (7), p.e68

2016

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

Nature chemical biology, 2024-05, Vol.20 (5), p.586

2024

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

Current opinion in structural biology, 2018-08, Vol.51, p.163-169

2018

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Computational design of vaccine immunogens

Current opinion in biotechnology, 2022-12, Vol.78, p.102821-102821, Article 102821

2022

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

Protein science, 2023-06, Vol.32 (6), p.e4653-n/a

2023

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Proteome-wide covalent ligand discovery in native biological systems

Nature (London), 2016-06, Vol.534 (7608), p.570-574

2016

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Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design

Journal of molecular biology, 2011-01, Vol.405 (1), p.284-297

2011

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

Ligand and Target Discovery by Fragment-Based Screening in Human Cells

RosettaSurf-A surface-centric computational design approach

A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells

Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells

A Computationally Designed Inhibitor of an Epstein-Barr Viral Bcl-2 Protein Induces Apoptosis in Infected Cells

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

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

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

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

Chemoproteomic profiling and discovery of protein electrophiles in human cells

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

Rules and mechanisms governing G protein coupling selectivity of GPCRs

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

A rational blueprint for the design of chemically-controlled protein switches

Oligomerization Profile of Human Transthyretin Variants with Distinct Amyloidogenicity

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

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

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

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

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

Computational design of vaccine immunogens

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

Proteome-wide covalent ligand discovery in native biological systems

Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design

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