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SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures
BackgroundThe relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a...
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How Does a Biopolymer (Protein) Fold into a Unique 3D Structure?
AbstractThe current state of the protein folding problem and other biopolymers folding is discussed. The concept of a multidimensional potential...
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FoldHSphere: deep hyperspherical embeddings for protein fold recognition
BackgroundCurrent state-of-the-art deep learning approaches for protein fold recognition learn protein embeddings that improve prediction performance...
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The S-component fold: a link between bacterial transporters and receptors
The processes of nutrient uptake and signal sensing are crucial for microbial survival and adaptation. Membrane-embedded proteins involved in these...
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Hsp104p: a protein disaggregase
All newly synthesized proteins must fold to their correct native conformation in order to function. That protein folding in the crowded...
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Protein–Protein Interactions: Co-immunoprecipitation
Proteins often do not function as single substances but rather as team players in a dynamic network. Growing evidences show that protein–protein...
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Establishment and characterization of immortalized human vocal fold fibroblast cell lines
PurposeVocal fold scarring is abnormal scar tissue in the lamina propria layer of the vocal fold. To facilitate investigation of vocal fold scarring,...
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Protein-Protein Binding Kinetics by Biolayer Interferometry
The specific kinetics and thermodynamics of protein-protein interactions underlie the molecular mechanisms of cellular functions; hence the...
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Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their...
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Protein features fusion using attributed network embedding for predicting protein-protein interaction
BackgroundProtein-protein interactions (PPIs) hold significant importance in biology, with precise PPI prediction as a pivotal factor in...
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Protein–Protein Interactions: Oxidative Bacterial Two Hybrid
Protein–protein interaction studies are essential to understand how proteins organize themselves into interaction networks and thus influence...
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Protein–Protein Interaction: Tandem Affinity Purification in Bacteria
The discovery of protein–protein interaction networks can lead to the unveiling of protein complex(es) forming cellular machinerie(s) or reveal...
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Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes
There are myriads of protein-protein complexes that form within the cell. In addition to classical binding events between globular domains, many...
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Spatial covariance analysis reveals the residue-by-residue thermodynamic contribution of variation to the CFTR fold
Although the impact of genome variation on the thermodynamic properties of function on the protein fold has been studied in vitro, it remains a...
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Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography
The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved...
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FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose...
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Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism
The constant emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants indicates the evolution and adaptation of the virus....
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Orchestrating copper binding: structure and variations on the cupredoxin fold
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was...
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The unfolded protein response unfolds
As a key organelle of protein targeting and secretion, the endoplasmic reticulum (ER) plays host to a wide variety of protein maturation steps...
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DeepFrag-k: a fragment-based deep learning approach for protein fold recognition
BackgroundOne of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning...
