Collision induced unfolding of isolated proteins in the gas phase: past, present, and future
Highlights•Collision induced unfolding (CIU) uses gas phase activation to probe
biomolecules.•CIU can detect subtle changes in protein structure, stability or …
biomolecules.•CIU can detect subtle changes in protein structure, stability or …
Biophysics of protein evolution and evolutionary protein biophysics
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
large datasets of sequences to infer their evolutionary relationships. Despite the importance …
ProtGPT2 is a deep unsupervised language model for protein design
Protein design aims to build novel proteins customized for specific purposes, thereby
holding the potential to tackle many environmental and biomedical problems. Recent …
holding the potential to tackle many environmental and biomedical problems. Recent …
Sequence-structure-function relationships in the microbial protein universe
For the past half-century, structural biologists relied on the notion that similar protein
sequences give rise to similar structures and functions. While this assumption has driven …
sequences give rise to similar structures and functions. While this assumption has driven …
Bridging themes: short protein segments found in different architectures
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer
function. Hence, protein evolution from preexisting building blocks has clear potential …
function. Hence, protein evolution from preexisting building blocks has clear potential …
The robustness and innovability of protein folds
A Toth-Petroczy, DS Tawfik - Current opinion in structural biology, 2014 - Elsevier
Highlights•Robustness relates to mutations having minimal effects on structure and
function.•Innovability means that beneficial functional changes are induced by few …
function.•Innovability means that beneficial functional changes are induced by few …
An ancient fingerprint indicates the common ancestry of Rossmann-fold enzymes utilizing different ribose-based cofactors
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is
one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes …
one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes …
A deep unsupervised language model for protein design
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 …
many environmental and biomedical problems. Recent progress in the field of natural …
Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains
The recent progress in the prediction of protein structures marked a historical milestone.
AlphaFold predicted 200 million protein models with an accuracy comparable to …
AlphaFold predicted 200 million protein models with an accuracy comparable to …
A survey of computational methods for protein function prediction
Rapid advances in high-throughout genome sequencing technologies have resulted in
millions of protein-encoding gene sequences with no functional characterization. Automated …
millions of protein-encoding gene sequences with no functional characterization. Automated …