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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 …
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 …
are functional proteins and domains that devoid stable secondary and/or tertiary structure …
AlphaFold predictions of fold-switched conformations are driven by structure memorization
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 …
accurately infer protein structure from sequence–may discern important features of folded …
Prottrans: Toward understanding the language of life through self-supervised learning
Computational biology and bioinformatics provide vast data gold-mines from protein
sequences, ideal for Language Models (LMs) taken from Natural Language Processing …
sequences, ideal for Language Models (LMs) taken from Natural Language Processing …
AlphaFold2 models indicate that protein sequence determines both structure and dynamics
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 …
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
Background Predicting protein function and structure from sequence is one important
challenge for computational biology. For 26 years, most state-of-the-art approaches …
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
Motivation Capturing long-range interactions between structural but not sequence neighbors
of proteins is a long-standing challenging problem in bioinformatics. Recently, long short …
of proteins is a long-standing challenging problem in bioinformatics. Recently, long short …
Understanding protein non-folding
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 …
form rigid 3-D structures under physiological conditions, either along their entire lengths or …
The importance of intrinsic disorder for protein phosphorylation
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 …
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
The structural, functional, and mechanistic characterization of several types of post‐
translational modifications (PTMs) is well‐documented. PTMs, however, may interact or …
translational modifications (PTMs) is well‐documented. PTMs, however, may interact or …