[HTML][HTML] AlphaFold and implications for intrinsically disordered proteins

KM Ruff, RV Pappu - Journal of molecular biology, 2021 - Elsevier
Accurate predictions of the three-dimensional structures of proteins from their amino acid
sequences have come of age. AlphaFold, a deep learning-based approach to protein …

Fuzziness and frustration in the energy landscape of protein folding, function, and assembly

S Gianni, MI Freiberger, P Jemth… - Accounts of chemical …, 2021 - ACS Publications
Conspectus Are all protein interactions fully optimized? Do suboptimal interactions
compromise specificity? What is the functional impact of frustration? Why does evolution not …

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

B Mészáros, G Erdős, Z Dosztányi - Nucleic acids research, 2018 - academic.oup.com
The structural states of proteins include ordered globular domains as well as intrinsically
disordered protein regions that exist as highly flexible conformational ensembles in …

MobiDB: intrinsically disordered proteins in 2021

D Piovesan, M Necci, N Escobedo… - Nucleic acids …, 2021 - academic.oup.com
The MobiDB database (URL: https://mobidb. org/) provides predictions and annotations for
intrinsically disordered proteins. Here, we report recent developments implemented in …

Analyzing protein disorder with IUPred2A

G Erdős, Z Dosztányi - Current protocols in bioinformatics, 2020 - Wiley Online Library
IUPred2A is a combined prediction tool designed to discover intrinsically disordered or
conditionally disordered proteins and protein regions. Intrinsically disordered regions exist …

DisProt in 2024: improving function annotation of intrinsically disordered proteins

MC Aspromonte, MV Nugnes, F Quaglia… - Nucleic Acids …, 2024 - academic.oup.com
Abstract DisProt (URL: https://disprot. org) is the gold standard database for intrinsically
disordered proteins and regions, providing valuable information about their functions. The …

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

Q Li, X Peng, Y Li, W Tang, J Zhu, J Huang… - Nucleic acids …, 2020 - academic.oup.com
Liquid-liquid phase separation (LLPS) leads to a conversion of homogeneous solution into a
dense phase that often resembles liquid droplets, and a dilute phase. An increasing number …

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 …

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

D Piovesan, F Tabaro, L Paladin, M Necci… - Nucleic acids …, 2018 - academic.oup.com
The MobiDB (URL: mobidb. bio. unipd. it) database of protein disorder and mobility
annotations has been significantly updated and upgraded since its last major renewal in …

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

F Quaglia, B Mészáros, E Salladini, A Hatos… - Nucleic acids …, 2022 - academic.oup.com
Abstract The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot. org)
is the major repository of manually curated annotations of intrinsically disordered proteins …