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dynamics simulation of the yeast spc alphafold2-multimer model  (Molecular Dynamics Inc)

 
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    Structured Review

    Molecular Dynamics Inc dynamics simulation of the yeast spc alphafold2-multimer model
    Dynamics Simulation Of The Yeast Spc Alphafold2 Multimer Model, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/alphafold2+multimer/alphafold2/pmc11579918-7-0-0
    Average 90 stars, based on 1 article reviews
    dynamics simulation of the yeast spc alphafold2-multimer model - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Sequencing:

    Article Title: Investigating the Nature of PRM:SH3 Interactions Using Artificial Intelligence and Molecular Dynamics
    Article Snippet: .. According to an editorial on data sharing and reproducibility of scientific results, all files related to AlphaFold2, including multiple sequence alignment (MSA) data, MSA coverage, predicted alignment errors, predicted contacts, predicted distograms, predicted local distance difference test (LDDT), structures from ranks 1 to 5, input sequences, and parameter files, have been deposited on GitHub at https://github.com/sejunkim6370/AlphaFold2-and-Molecular-Dynamics . ..

    other:

    Article Title: AlphaFold3: An Overview of Applications and Performance Insights
    Article Snippet: Molecular dynamics simulations were further performed on AlphaFold3’s models to assess the dynamic stability of the predicted dimers and resistance-associated mutations, and improved tubulin dimerization by stabilizing the interfacial interactions between α - and β -tubulin subunits was detected.

    Article Title: Improving the Soluble Expression of Sweet Protein Thaumatin II through Directed Evolution in Escherichia coli .
    Article Snippet: Thaumatin is a natural sweet protein valued for its intense sweetness, long-lasting effect, low-calorie content, and safety.. However, limited solubility and low yields hinder microbial fermentation.. To overcome these challenges, we engineered Escherichia coli to express thaumatin II and implemented three strategies to improve its solubility.

    Article Title: Substrate recognition in Bacillus anthracis sortase B beyond its canonical pentapeptide binding motif and use in sortase-mediated ligation
    Article Snippet: Molecular dynamics simulations of SrtB AlphaFold2 models.

    Article Title: AlphaFold3: An Overview of Applications and Performance Insights
    Article Snippet: Molecular dynamics simulations were further performed on AlphaFold3’s models to assess the dynamic stability of the predicted dimers and resistance-associated mutations, and improved tubulin dimerization by stabilizing the interfacial interactions between α- and β-tubulin subunits was detected.

    Article Title: Exploring FAM13A-N-Myc interactions to uncover potential targets in MYCN-amplified neuroblastoma: a study of protein interactions and molecular dynamics simulations
    Article Snippet: Fig. 7 Molecular dynamics simulation optimizes the predicted structure of FAM13A for accurate protein-protein docking studies. (A) Alphafold v2.3.2 to predict the protein structure of FAM13A. (B-E) The Ramachandran plots were then utilized to assess the accuracy of the FAM13A predicted structures. (F-G) The results of RMSD and RoG show that the protein structure of FAM13A tends to be stable. (H) Free energy topography of FAM13A after stabilization. (I-L) The Ramachandran plots were then utilized to assess the accuracy of the FAM13A optimized structures

    Article Title: Scanning Tunneling Microscope Measurement of Proteasome Conductance.
    Article Snippet: An AlphaFold3 model with both the N- and C-termini, relaxed by a brief molecular dynamics simulation, is shown in Figure 6.

    Fluorescence:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Förster Resonance Energy Transfer:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Cryo-Electron Microscopy:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Software:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Nuclear Magnetic Resonance:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Isothermal Titration Calorimetry:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Circular Dichroism:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Mass Spectrometry:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..

    Mutagenesis:

    Article Title: Christian Bohr. Discoverer of Homotropic and Heterotopic Allostery
    Article Snippet: .. Structure–activity‐relations, SARs, X‐ray methods, fluorescence resonance energy transfer (FRET), cryoelectron‐microscopy (cryo‐EM), deep learning (DL) for instance with AlphaFold 2 and 3, molecular dynamics (MD), software for molecular dynamics, gaussian accelerated molecular dynamics (GaMD), Markov‐state‐models, free energy Profiling Workflow (GLOW), quantum mechanics (QM), nuclear magnetic resonance (NMR), temperature‐dependent Isothermal Titration Calorimetry (ITC), Circular Dichroism (CD) spectroscopy, hydrogen exchange (HX), mass spectrometry (MS), and genetic manipulations with full‐protein alanine‐scanning mutagenesis. ..



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    Potential binding sites of the pHAT domains to nucleosomes, highlighting proximity and spacing of the H3K36 residues ( a ) as well as the H3K36 and H4K 5,8,12, and 16 residues ( b ) in the nucleosome (PDBID:1kx5: gray). OGA is colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and HAT-like domain: green. The distance between K36 residues (red) is 73.5 Å, and the total distance between pHAT densities is 107 Å (green). The distance between the K36 residue and the H4K 5,8,12,16 is 72.8 Å (pink). c OGA-L pHAT binding to histone modifications such as H3K36 Me and acetylated H4 tails would facilitate recruitment to sites of active transcription and DNA repair. The structural features identified for OGA-L are likely to increase the local concentration of tihe OGA-L and allow flexible movement of the catalytic domain to facilitate O- GlcNAc removal from proteins in proximity. The OGA model is shown with unstructured linkers added from the <t>Alphafold2</t> colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and pHAT domain, green.
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    Image Search Results


    Potential binding sites of the pHAT domains to nucleosomes, highlighting proximity and spacing of the H3K36 residues ( a ) as well as the H3K36 and H4K 5,8,12, and 16 residues ( b ) in the nucleosome (PDBID:1kx5: gray). OGA is colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and HAT-like domain: green. The distance between K36 residues (red) is 73.5 Å, and the total distance between pHAT densities is 107 Å (green). The distance between the K36 residue and the H4K 5,8,12,16 is 72.8 Å (pink). c OGA-L pHAT binding to histone modifications such as H3K36 Me and acetylated H4 tails would facilitate recruitment to sites of active transcription and DNA repair. The structural features identified for OGA-L are likely to increase the local concentration of tihe OGA-L and allow flexible movement of the catalytic domain to facilitate O- GlcNAc removal from proteins in proximity. The OGA model is shown with unstructured linkers added from the Alphafold2 colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and pHAT domain, green.

    Journal: Communications Chemistry

    Article Title: Human O- GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains

    doi: 10.1038/s42004-025-01813-7

    Figure Lengend Snippet: Potential binding sites of the pHAT domains to nucleosomes, highlighting proximity and spacing of the H3K36 residues ( a ) as well as the H3K36 and H4K 5,8,12, and 16 residues ( b ) in the nucleosome (PDBID:1kx5: gray). OGA is colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and HAT-like domain: green. The distance between K36 residues (red) is 73.5 Å, and the total distance between pHAT densities is 107 Å (green). The distance between the K36 residue and the H4K 5,8,12,16 is 72.8 Å (pink). c OGA-L pHAT binding to histone modifications such as H3K36 Me and acetylated H4 tails would facilitate recruitment to sites of active transcription and DNA repair. The structural features identified for OGA-L are likely to increase the local concentration of tihe OGA-L and allow flexible movement of the catalytic domain to facilitate O- GlcNAc removal from proteins in proximity. The OGA model is shown with unstructured linkers added from the Alphafold2 colored by domain: catalytic domain, dark blue; stalk, yellow; linker, and pHAT domain, green.

    Article Snippet: Additional data compared in this study from the protein databank: Alphafold2 Multimer, PDB ID: 5M7R, PDB ID: 5VVO, PDB ID:5UHK, PDB ID: 5M7S, PDBID:5UN9, PDB ID:5UHL, PDB ID: 5M7T, PDB ID: 5UHO, PDB ID: 8P0L, PDB ID: 9BA8, 9BA9, PDB ID: 1KX5 .

    Techniques: Binding Assay, Residue, Concentration Assay

    The plot provides a visual representation of how well the input sequence aligns with other related sequences across the entire sequence. Except at positions 500 and 1220, a significant portion of the protein has moderate sequence identity. AF2M: AlphaFold2 Multimer

    Journal: Cureus

    Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

    doi: 10.7759/cureus.82254

    Figure Lengend Snippet: The plot provides a visual representation of how well the input sequence aligns with other related sequences across the entire sequence. Except at positions 500 and 1220, a significant portion of the protein has moderate sequence identity. AF2M: AlphaFold2 Multimer

    Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

    Techniques: Sequencing

    PAE plots assess structural confidence and domain flexibility. Blue (low PAE) indicates high-confidence intra-domain folding; red (high PAE) shows uncertain inter-domain positioning. Diagonal blue regions confirm well-defined COPA and HAQ-STING domains. Off-diagonal red regions reflect flexible or variable inter-domain orientations. Model 1 (rank_1) shows slightly higher structural definition. PAE: Predicted aligned error; AF2M: AlphaFold2 Multimer; STING: Stimulator of interferon genes

    Journal: Cureus

    Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

    doi: 10.7759/cureus.82254

    Figure Lengend Snippet: PAE plots assess structural confidence and domain flexibility. Blue (low PAE) indicates high-confidence intra-domain folding; red (high PAE) shows uncertain inter-domain positioning. Diagonal blue regions confirm well-defined COPA and HAQ-STING domains. Off-diagonal red regions reflect flexible or variable inter-domain orientations. Model 1 (rank_1) shows slightly higher structural definition. PAE: Predicted aligned error; AF2M: AlphaFold2 Multimer; STING: Stimulator of interferon genes

    Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

    Techniques:

    pIDDT scores indicate high local structure confidence (70–90) for most residues, with dips below 50 marking flexible or disordered regions. A black line at position 1220 highlights a domain boundary or interaction site with notable structural variability. pIDDT: Predicted intrinsic distance difference test; AF2M: AlphaFold2 Multimer

    Journal: Cureus

    Article Title: Interaction Between HAQ-STING Mutation and COPA: Protection Against COPA Syndrome

    doi: 10.7759/cureus.82254

    Figure Lengend Snippet: pIDDT scores indicate high local structure confidence (70–90) for most residues, with dips below 50 marking flexible or disordered regions. A black line at position 1220 highlights a domain boundary or interaction site with notable structural variability. pIDDT: Predicted intrinsic distance difference test; AF2M: AlphaFold2 Multimer

    Article Snippet: In the current study, AlphaFold2 Multimer (AF2M) version 3 (DeepMind, London, UK) was used to assess the interaction between the COPA, STING, and HAQ-STING proteins.

    Techniques: