AIMC Topic: Protein Domains

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The EMC acts as a chaperone for membrane proteins.

Nature communications Aug 2, 2025
Structure formation of membrane proteins is error-prone and thus requires chaperones that oversee this essential process in cell biology. The ER membrane protein complex (EMC) is well-defined as a transmembrane domain (TMD) insertase. In this study, ...
Machine Learning Protein Binding Membrane Proteins Humans Saccharomyces cerevisiae Proteins Molecular Chaperones Endoplasmic Reticulum Protein Domains Saccharomyces cerevisiae Lipid Bilayers
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Consensus structure prediction of A. thaliana's MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics.

PloS one Jul 15, 2025
Multiple C2 Domains and Transmembrane region Proteins (MCTPs) in plants have been identified as important functional and structural components of plasmodesmata cytoplasmic bridges, which are vital for cell-cell communication. MCTPs are endoplasmic re...
Deep Learning Membrane Proteins Protein Domains Arabidopsis Molecular Dynamics Simulation Endoplasmic Reticulum Protein Conformation Arabidopsis Proteins
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M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics May 5, 2025
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...
Databases, Protein Deep Learning Models, Molecular Computational Biology Protein Domains Algorithms Proteins Protein Conformation
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Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design.

Journal of chemical information and modeling May 1, 2025
Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges ...
Adenosine Triphosphate Binding Sites HSP90 Heat-Shock Proteins Protein Binding Protein Domains Peptides Molecular Dynamics Simulation Humans Molecular Docking Simulation Machine Learning Drug Design
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DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions.

Journal of molecular biology Apr 4, 2025
Proteins often perform biological functions by forming complexes, thereby accurately predicting the structure of protein complexes is crucial to understanding and mastering their functions, as well as facilitating drug discovery. Protein monomeric st...
Internet Protein Conformation Deep Learning Computational Biology Proteins Databases, Protein Models, Molecular Protein Domains Software
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Models, Molecular Protein Domains Amino Acid Sequence Cluster Analysis Proteins Databases, Protein Protein Conformation Sequence Alignment Sequence Analysis, Protein Algorithms Deep Learning Computational Biology
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Lessons from Deep Learning Structural Prediction of Multistate Multidomain Proteins-The Case Study of Coiled-Coil NOD-like Receptors.

International journal of molecular sciences Jan 9, 2025
We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain...
Arabidopsis Protein Domains Protein Conformation Protein Structure, Secondary Computational Biology Deep Learning Models, Molecular NLR Proteins
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DPFunc: accurately predicting protein function via deep learning with domain-guided structure information.

Nature communications Jan 2, 2025
Computational methods for predicting protein function are of great significance in understanding biological mechanisms and treating complex diseases. However, existing computational approaches of protein function prediction lack interpretability, mak...
Deep Learning Protein Domains Databases, Protein Humans Computational Biology Algorithms Proteins Structure-Activity Relationship Protein Conformation Models, Molecular
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Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay.

European biophysics journal : EBJ Nov 29, 2024
Human Snk is an evolutionarily conserved serine/threonine kinase essential for the maintenance of endocrine stability. The protein consists of a N-terminal catalytic domain and a C-terminal polo-box domain (PBD) that determines subcellular localizati...
Molecular Dynamics Simulation Protein Binding Amino Acid Sequence Protein Serine-Threonine Kinases Phosphopeptides Thermodynamics Humans Protein Domains Machine Learning Drug Design
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Molecular Dynamics Simulation RNA Machine Learning Substrate Specificity DNA CRISPR-Associated Protein 9 CRISPR-Cas Systems Bacterial Proteins Francisella Protein Domains
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