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Molecular Dynamics Inc alphafold multimer v 2 3 structures
Alphafold Multimer V 2 3 Structures, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/alphafold+2/2+3+alphafold+multimer+structures+v/pmc13121041-309-9-0
Average 86 stars, based on 1 article reviews
alphafold multimer v 2 3 structures - by Bioz Stars, 2026-10
86/100 stars

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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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Deepmind Technologies Ltd alphafold multimer version 2 3 2
A. Protein diagrams of RON6, RON10, GRA7 and GRA15 indicating the position of their TRAF6-binding motifs with accompanying multiple sequence alignment showing their presence in different Toxoplasma strains and Coccidian species. B. <t>AlphaFold</t> model of TRAF6 MATH domain with TRAF6-binding motif from RON10. Right panels display the potential hydrogen bond network at the interaction interface (top) and secondary structure adopted by the TRAF6-binding motif (bottom). C. RON10 TRAF6 motif testing. MST traces (top graph) and dose-response curves (bottom panel) of TRAF6 MATH domain binding to RON10 TRAF6 motif containing peptide (left) and the E>S mutant (right). In the MST traces, the cold region is set at 0 s (blue) and the hot detection region at 5 s (red). D . Same as in A, but for the GRA15 TRAF6 motif and the E>S motif mutant.
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A. Protein diagrams of RON6, RON10, GRA7 and GRA15 indicating the position of their TRAF6-binding motifs with accompanying multiple sequence alignment showing their presence in different Toxoplasma strains and Coccidian species. B. AlphaFold model of TRAF6 MATH domain with TRAF6-binding motif from RON10. Right panels display the potential hydrogen bond network at the interaction interface (top) and secondary structure adopted by the TRAF6-binding motif (bottom). C. RON10 TRAF6 motif testing. MST traces (top graph) and dose-response curves (bottom panel) of TRAF6 MATH domain binding to RON10 TRAF6 motif containing peptide (left) and the E>S mutant (right). In the MST traces, the cold region is set at 0 s (blue) and the hot detection region at 5 s (red). D . Same as in A, but for the GRA15 TRAF6 motif and the E>S motif mutant.

Journal: bioRxiv

Article Title: Short linear motifs - Unexplored players driving Toxoplasma gondii infection

doi: 10.64898/2026.01.12.699020

Figure Lengend Snippet: A. Protein diagrams of RON6, RON10, GRA7 and GRA15 indicating the position of their TRAF6-binding motifs with accompanying multiple sequence alignment showing their presence in different Toxoplasma strains and Coccidian species. B. AlphaFold model of TRAF6 MATH domain with TRAF6-binding motif from RON10. Right panels display the potential hydrogen bond network at the interaction interface (top) and secondary structure adopted by the TRAF6-binding motif (bottom). C. RON10 TRAF6 motif testing. MST traces (top graph) and dose-response curves (bottom panel) of TRAF6 MATH domain binding to RON10 TRAF6 motif containing peptide (left) and the E>S mutant (right). In the MST traces, the cold region is set at 0 s (blue) and the hot detection region at 5 s (red). D . Same as in A, but for the GRA15 TRAF6 motif and the E>S motif mutant.

Article Snippet: The local installation of AlphaFold Multimer version 2.3.2 was run using the following parameters and following Alphafold GitHub instructions ( https://github.com/deepmind/alphafold#running-alphafold ): --model_preset=multimer \ --db_preset=full_dbs \ --max_template_date=2020-05-14 \ --num_multimer_predictions_per_model=1 \ --use_gpu_relax=True \ -- bfd_database_path=/mnt/storage/alphafold/v232/bfd/bfd_metaclust_clu_complete_id30_c90 _final_seq.sorted_opt \ --mgnify_database_path=/mnt/storage/alphafold/v232/mgnify/mgy_clusters_2022_05.fa \ --obsolete_pdbs_path=/mnt/storage/alphafold/v232/pdb_mmcif/obsolete.dat \ --pdb_seqres_database_path=/mnt/storage/alphafold/v232/pdb_seqres/pdb_seqres.txt \ --template_mmcif_dir=/mnt/storage/alphafold/v232/pdb_mmcif/mmcif_files \ --uniprot_database_path=/mnt/storage/alphafold/v232/uniprot/uniprot.fasta \ --uniref90_database_path=/mnt/storage/alphafold/v232/uniref90/uniref90.fasta \ --uniref30_database_path=/mnt/storage/alphafold/v232/uniref30/UniRef30_2021_03 \ --use_precomputed_msas=True

Techniques: Binding Assay, Sequencing, Mutagenesis