ProtGPT2 is a deep unsupervised language model for protein design

N Ferruz, S Schmidt, B Höcker - Nature communications, 2022 - nature.com
Protein design aims to build novel proteins customized for specific purposes, thereby
holding the potential to tackle many environmental and biomedical problems. Recent …

A deep unsupervised language model for protein design

N Ferruz, S Schmidt, B Höcker - BioRxiv, 2022 - biorxiv.org
Protein design aims to build new proteins from scratch thereby holding the potential to tackle
many environmental and biomedical problems. Recent progress in the field of natural …

Retracing the evolution of a modern periplasmic binding protein

F Michel, S Romero‐Romero, B Höcker - Protein Science, 2023 - Wiley Online Library
Investigating the evolution of structural features in modern multidomain proteins helps to
understand their immense diversity and functional versatility. The class of periplasmic …

De novo design of triosephosphate isomerases using generative language models

S Romero-Romero, AE Braun, T Kossendey, N Ferruz… - bioRxiv, 2024 - biorxiv.org
The design of proteins with tailored functions is of immense interest to biotechnology,
medicine, and the chemical industry. While protein design is rapidly evolving with the use of …

[PDF][PDF] Structures of permuted halves of a modern ribose-binding protein

F Michel, S Shanmugaratnam… - … Section D: Structural …, 2023 - journals.iucr.org
Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular
transport of various ligands. They have been used as model systems to study mechanisms …

Molecular handcraft of a well‐folded protein chimera

S Toledo‐Patiño, SK Goetz, S Shanmugaratnam… - FEBS …, 2024 - Wiley Online Library
Modular assembly is a compelling pathway to create new proteins, a concept supported by
protein engineering and millennia of evolution. Natural evolution provided a repository of …

Folding and Evolution of a Repeat Protein on the Ribosome

JA León-González, P Flatet… - Frontiers in Molecular …, 2022 - frontiersin.org
Life on earth is the result of the work of proteins, the cellular nanomachines that fold into
elaborated 3D structures to perform their functions. The ribosome synthesizes all the …

Explainable Deep Generative Models, Ancestral Fragments, and Murky Regions of the Protein Structure Universe

EJ Draizen, C Mura, PE Bourne - bioRxiv, 2022 - biorxiv.org
Modern proteins did not arise abruptly, as singular events, but rather over the course of at
least 3.5 billion years of evolution. Can machine learning teach us how this occurred? The …

[PDF][PDF] Fragment and Binding Mode Conservation with the Fuzzle database: A Case Study with Periplasmic Binding Proteins.

S Dhingra, J Krumm, N Ferruz, B Höcker - researchgate.net
In recent years, protein evolutionary studies have shifted from protein domains considered
as the basic evolutionary units to sub-domain sized fragments as the basis of diverse …