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 …

Intrinsic disorder and posttranslational modifications: the darker side of the biological dark matter

AL Darling, VN Uversky - Frontiers in genetics, 2018 - frontiersin.org
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs)
are functional proteins and domains that devoid stable secondary and/or tertiary structure …

AlphaFold predictions of fold-switched conformations are driven by structure memorization

D Chakravarty, JW Schafer, EA Chen, JF Thole… - Nature …, 2024 - nature.com
Recent work suggests that AlphaFold (AF)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …

Prottrans: Toward understanding the language of life through self-supervised learning

A Elnaggar, M Heinzinger, C Dallago… - IEEE transactions on …, 2021 - ieeexplore.ieee.org
Computational biology and bioinformatics provide vast data gold-mines from protein
sequences, ideal for Language Models (LMs) taken from Natural Language Processing …

AlphaFold2 models indicate that protein sequence determines both structure and dynamics

HB Guo, A Perminov, S Bekele, G Kedziora… - Scientific reports, 2022 - nature.com
Abstract AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can
visualize, analyze and interpret the structures and functions of all proteins solely from their …

Modeling aspects of the language of life through transfer-learning protein sequences

M Heinzinger, A Elnaggar, Y Wang, C Dallago… - BMC …, 2019 - Springer
Background Predicting protein function and structure from sequence is one important
challenge for computational biology. For 26 years, most state-of-the-art approaches …

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks

J Hanson, Y Yang, K Paliwal, Y Zhou - Bioinformatics, 2017 - academic.oup.com
Motivation Capturing long-range interactions between structural but not sequence neighbors
of proteins is a long-standing challenging problem in bioinformatics. Recently, long short …

Understanding protein non-folding

VN Uversky, AK Dunker - Biochimica et Biophysica Acta (BBA)-Proteins …, 2010 - Elsevier
This review describes the family of intrinsically disordered proteins, members of which fail to
form rigid 3-D structures under physiological conditions, either along their entire lengths or …

The importance of intrinsic disorder for protein phosphorylation

LM Iakoucheva, P Radivojac, CJ Brown… - Nucleic acids …, 2004 - academic.oup.com
Reversible protein phosphorylation provides a major regulatory mechanism in eukaryotic
cells. Due to the high variability of amino acid residues flanking a relatively limited number of …

The structural and functional signatures of proteins that undergo multiple events of post‐translational modification

V Pejaver, WL Hsu, F **n, AK Dunker… - Protein …, 2014 - Wiley Online Library
The structural, functional, and mechanistic characterization of several types of post‐
translational modifications (PTMs) is well‐documented. PTMs, however, may interact or …