Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability

Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

Classification of intrinsically disordered regions and proteins

R Van Der Lee, M Buljan, B Lang, RJ Weatheritt… - Chemical …, 2014 - ACS Publications
Over the past decade, we have observed a massive increase in the amount of information
describing protein sequences from a variety of organisms. 1, 2 While this may reflect the …

IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation

G Erdős, M Pajkos, Z Dosztányi - Nucleic acids research, 2021 - academic.oup.com
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-
defined conformation. They carry out important biological functions with multifaceted roles …

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 …

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 …

In situ analysis of osmolyte mechanisms of proteome thermal stabilization

M Pepelnjak, B Velten, N Näpflin, T von Rosen… - Nature Chemical …, 2024 - nature.com
Organisms use organic molecules called osmolytes to adapt to environmental conditions. In
vitro studies indicate that osmolytes thermally stabilize proteins, but mechanisms are …

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

DT Jones, D Cozzetto - Bioinformatics, 2015 - academic.oup.com
Motivation: A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions
(IDRs), which act in unfolded states or by undergoing transitions between structured and …

Intrinsically disordered proteins and intrinsically disordered protein regions

CJ Oldfield, AK Dunker - Annual review of biochemistry, 2014 - annualreviews.org
Intrinsically disordered proteins (IDPs) and IDP regions fail to form a stable structure, yet
they exhibit biological activities. Their mobile flexibility and structural instability are encoded …

[HTML][HTML] Protein stability: a crystallographer's perspective

MC Deller, L Kong, B Rupp - Structural Biology and Crystallization …, 2016 - journals.iucr.org
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food
industries, in addition to being a daily consideration for academic researchers studying …

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Y Yang, J Gao, J Wang, R Heffernan… - Briefings in …, 2018 - academic.oup.com
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …