alphafold2 multimer v3 0  (Deepmind Technologies Ltd)

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

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

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:

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:

Journal: International Journal of Molecular Sciences

Article Title: A Computational Approach in the Systematic Search of the Interaction Partners of Alternatively Spliced TREM2 Isoforms †

doi: 10.3390/ijms25179667

Figure Lengend Snippet: General workflow diagram. In step 1, proteome-wide screening by ProteinPrompt was used to identify the prospective interaction partners for TREM2 isoforms. In step 2, independent modeling by PEPPI was used to validate step 1’s predictions. In step 3, the interaction partners identified in step 1 and validated in step 2 were built into a heterodimeric complex with the corresponding TREM isoform by AlphaFold2 Multimer.

Article Snippet: AlphaFold2 Multimer v3 is an extension of AlphaFold2, a computational structural biology program developed by Google’s artificial intelligence arm Deepmind and a newer iteration of AlphaFold [ ].

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: A Computational Approach in the Systematic Search of the Interaction Partners of Alternatively Spliced TREM2 Isoforms †

doi: 10.3390/ijms25179667

Figure Lengend Snippet: AlphaFold2 Multimer visualization of the dimeric complexes formed by TREM2 alternatively spliced isoforms and the newfound interaction partners with part of the interacting interface zoomed in: ( A ) TREM2△exon2 (dark green) and CD9 (orange), ( B ) TREM2△exon4 (dark green) and CD9 (orange), ( C ) TREM2△exon5 (dark green) and CALM (orange)—and structural superposition between canonical TREM2 (red) and the isoforms—( D ) between canonical TREM2 and TREM2△exon2, ( E ) between canonical TREM2 and TREM2△exon4, ( F ) between canonical TREM2 and TREM2△exon5.

Article Snippet: AlphaFold2 Multimer v3 is an extension of AlphaFold2, a computational structural biology program developed by Google’s artificial intelligence arm Deepmind and a newer iteration of AlphaFold [ ].

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: A Computational Approach in the Systematic Search of the Interaction Partners of Alternatively Spliced TREM2 Isoforms †

doi: 10.3390/ijms25179667

Figure Lengend Snippet: The interacting interfaces in AlphaFold2 Multimer’s three heterodimeric complexes.

Article Snippet: AlphaFold2 Multimer v3 is an extension of AlphaFold2, a computational structural biology program developed by Google’s artificial intelligence arm Deepmind and a newer iteration of AlphaFold [ ].

Techniques: