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Advanced Technologies for Protein Complex Production and Characterization Volume II
This edited volume discusses the identification, discovery, characterization, structure determination and modeling of multicomponent macromolecular...
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Topological links in predicted protein complex structures reveal limitations of AlphaFold
AlphaFold is making great progress in protein structure prediction, not only for single-chain proteins but also for multi-chain protein complexes....
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Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure
AbstractProtein complexes perform diverse biological functions, and obtaining their three-dimensional structure is critical to understanding and...
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Small protein complex prediction algorithm based on protein–protein interaction network segmentation
BackgroundIdentifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein...
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A computational framework for the inference of protein complex remodeling from whole-proteome measurements
Protein complexes are responsible for the enactment of most cellular functions. For the protein complex to form and function, its subunits often need...
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Molecular basis of the TRAP complex function in ER protein biogenesis
The translocon-associated protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the...
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BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix
AbstractProtein complex structure prediction is an important problem in computational biology. While significant progress has been made for protein...
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Molecular complex detection in protein interaction networks through reinforcement learning
BackgroundProteins often assemble into higher-order complexes to perform their biological functions. Such protein–protein interactions (PPI) are...
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TAF2, within the TFIID complex, regulates the expression of a subset of protein-coding genes
TFIID, one of the general transcription factor (GTF), regulates transcriptional initiation of protein-coding genes through direct binding to promoter...
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Multi-domain and complex protein structure prediction using inter-domain interactions from deep learning
Accurately capturing domain-domain interactions is key to understanding protein function and designing structure-based drugs. Although AlphaFold2 has...
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Role of the V2R–βarrestin–Gβγ complex in promoting G protein translocation to endosomes
Classically, G protein-coupled receptors (GPCRs) promote signaling at the plasma membrane through activation of heterotrimeric Gαβγ proteins,...
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Explicit versus implicit consideration of binding partners in protein–protein complex to elucidate intrinsic dynamics
The binding of many proteins to their protein partners is tightly regulated via control of their relative intrinsic dynamics during the binding...
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Preparation and Utilization of a Versatile GFP-Protein Trap-Like System for Protein Complex Immunoprecipitation in Plants
Protein complex immunoprecipitation (co-IP) is an in vitro technique used to study protein–protein interaction between two or more proteins. This...
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Computational Study of Conformational Changes in Intrinsically Disordered Regions During Protein-Protein Complex Formation
Intrinsically Disordered Regions (IDRs) even though they cannot form a defined three-dimensional structure play a pivotal role in modulating cellular...
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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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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
To enhance the AlphaFold-Multimer-based protein complex structure prediction, we developed a quaternary structure prediction system (MULTICOM) to...
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Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data
Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single-...
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The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium
The efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to...
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A hybrid TIM complex mediates protein import into hydrogenosomes of Trichomonas vaginalis
BackgroundHydrogenosomes are a specific type of mitochondria that have adapted for life under anaerobiosis. Limited availability of oxygen has...
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Structural inventory of cotranslational protein folding by the eukaryotic RAC complex
The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with...
