The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

V Agarwal, AC McShan - Nature Chemical Biology, 2024 - nature.com
Artificial intelligence-driven advances in protein structure prediction in recent years have
raised the question: has the protein structure-prediction problem been solved? Here, with a …

Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins

L Kurgan, G Hu, K Wang, S Ghadermarzi, B Zhao… - Nature …, 2023 - nature.com
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using
computational predictions from primary structures, complements secondary and tertiary …

Conformational ensembles of the human intrinsically disordered proteome

G Tesei, AI Trolle, N Jonsson, J Betz, FE Knudsen… - Nature, 2024 - nature.com
Intrinsically disordered proteins and regions (collectively, IDRs) are pervasive across
proteomes in all kingdoms of life, help to shape biological functions and are involved in …

MobiDB: 10 years of intrinsically disordered proteins

D Piovesan, A Del Conte, D Clementel… - Nucleic acids …, 2023 - academic.oup.com
The MobiDB database (URL: https://mobidb. org/) is a knowledge base of intrinsically
disordered proteins. MobiDB aggregates disorder annotations derived from the literature …

Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2

TR Alderson, I Pritišanac, Đ Kolarić, AM Moses… - Proceedings of the …, 2023 - pnas.org
The AlphaFold Protein Structure Database contains predicted structures for millions of
proteins. For the majority of human proteins that contain intrinsically disordered regions …

The HIV capsid mimics karyopherin engagement of FG-nucleoporins

CF Dickson, S Hertel, AJ Tuckwell, N Li, J Ruan… - Nature, 2024 - nature.com
HIV can infect non-dividing cells because the viral capsid can overcome the selective barrier
of the nuclear pore complex and deliver the genome directly into the nucleus,. Remarkably …

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

H Ghafouri, T Lazar, A Del Conte… - Nucleic acids …, 2024 - academic.oup.com
Abstract The Protein Ensemble Database (PED)(URL: https://proteinensemble. org) is the
primary resource for depositing structural ensembles of intrinsically disordered proteins. This …

[HTML][HTML] AlphaFold2: a role for disordered protein/region prediction?

CJ Wilson, WY Choy, M Karttunen - International Journal of Molecular …, 2022 - mdpi.com
The development of AlphaFold2 marked a paradigm-shift in the structural biology
community. Herein, we assess the ability of AlphaFold2 to predict disordered regions …

Critical assessment of protein intrinsic disorder prediction (CAID)‐Results of round 2

AD Conte, M Mehdiabadi, A Bouhraoua… - Proteins: Structure …, 2023 - Wiley Online Library
Protein intrinsic disorder (ID) is a complex and context‐dependent phenomenon that covers
a continuum between fully disordered states and folded states with long dynamic regions …

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

A Del Conte, A Bouhraoua, M Mehdiabadi… - Nucleic acids …, 2023 - academic.oup.com
Intrinsic disorder (ID) in proteins is well-established in structural biology, with increasing
evidence for its involvement in essential biological processes. As measuring dynamic ID …