alphafold pipeline  (SIB Swiss Institute of Bioinformatics)

Journal: Proteomics

Article Title: Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study

doi: 10.1002/pmic.202200323

Figure Lengend Snippet: Classification performance of AlphaFold2 models predicted for the physiological and non-physiological homo dimers of the benchmark dataset. This is evaluated on the subset of 1480 targets for which results were produced with all AlphaFold2 versions. Column 1 lists the version of AlphaFold used for the predictions, and the score used to quantify the similarity between the AlphaFold2 predicted model, and the homodimer structures of the corresponding benchmark entry (see Main text for detail). Column 2 lists the Area Under the Curve (AUC) of the ROCs computed using the listed scores. Columns 3 and 4 list the mean and median values for the computed scores considering only the physiological dimers. Those for the non-physiological dimers are not reported, as AlphaFold2 tends to predict alternative association modes for a significant fraction of these dimers, as expected.

Article Snippet: G.T., L.P., and T.S. acknowledge the contributions of Gabriel Studer in setting up the AlphaFold pipeline for our analysis, sciCORE at the University of Basel for providing computational resources and system administration support, and funding from the SIB Swiss Institute of Bioinformatics and the Biozentrum PhD Fellowships.

Techniques: Produced

Journal: Molecules

Article Title: Computational Modeling Study of the Binding of Aging and Non-Aging Inhibitors with Neuropathy Target Esterase

doi: 10.3390/molecules28237747

Figure Lengend Snippet: The constructed NEST models. ( A ) The sequence alignment results between PlpD and NEST. Identical residues have been boxed in the black color. Secondary structures of PlpD (shown on the top of the sequence) and two NEST models built by MODELLER 10.3 and the AlphaFold2 (shown below the sequence) are displayed. β-strands are shown as arrows colored in cream and α-helices are shown as rectangles colored in blue. ( B , C ) The overall structure models of NEST built by MODELLER 10.3 ( B ) and AlphaFold2 ( C ). ( D , E ) The overlay of AlphaFold model and MODELLER model ( D ) and the overlay of the MODELLER model with the PlpD structure ( E ). The PlpD structure, the MODELLER model, and the AlphaFold model are colored blue, green, and cream, respectively.

Article Snippet: Another model of NEST was predicted by using the AlphaFold Monomer v2.0 pipeline from AlphaFold Protein Structure Database ( https://alphafold.ebi.ac.uk/ accessed on 24 October 2022) developed by DeepMind and EMBL-EBI [ ].

Techniques: Construct, Sequencing, Cream

Journal: Molecules

Article Title: Computational Modeling Study of the Binding of Aging and Non-Aging Inhibitors with Neuropathy Target Esterase

doi: 10.3390/molecules28237747

Figure Lengend Snippet: The overlay of the overall structures of NEST models and important active residues. ( A , B ) The enlarged view of the predicted active site of NEST. Important residues, such as Ser1014, Asp1008, and Asp1134 are shown as sticks. Distances between Ser1014 Oγ and Asp1008 O δ2 and Ser966 Oγ and Asp1134 O δ2 are shown as dotted lines. ( C , D ) The overlay of important residues (including Ser1014, Asp1134, and oxyanion hole residues between AlphaFold model and MODELLER model ( C ) and between the MODELLER model and the PlpD ( D ). The PlpD structure, the MODELLER model, and the AlphaFold model are colored blue, green, and cream, respectively.

Article Snippet: Another model of NEST was predicted by using the AlphaFold Monomer v2.0 pipeline from AlphaFold Protein Structure Database ( https://alphafold.ebi.ac.uk/ accessed on 24 October 2022) developed by DeepMind and EMBL-EBI [ ].

Techniques: Cream

Journal: Molecules

Article Title: Computational Modeling Study of the Binding of Aging and Non-Aging Inhibitors with Neuropathy Target Esterase

doi: 10.3390/molecules28237747

Figure Lengend Snippet: Predicted CDOCKER energy of 5 NTE inhibitors and 1 substrate with NEST AlphaFold model by molecular docking.

Article Snippet: Another model of NEST was predicted by using the AlphaFold Monomer v2.0 pipeline from AlphaFold Protein Structure Database ( https://alphafold.ebi.ac.uk/ accessed on 24 October 2022) developed by DeepMind and EMBL-EBI [ ].

Techniques:

Journal: Frontiers in Microbiology

Article Title: The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms

doi: 10.3389/fmicb.2023.1090534

Figure Lengend Snippet: The key role of C-terminal domain of Mycobacterium tuberculosis ( M. tb ) FadD23. (A) The difference in the rate of enzyme activity of the mutants. (B) Stereo representation of the hydrophobic ATP-FadD23 complex. (C) Bottom view of the structure predicted by AlphaFold2 compared with that of FadD23. Blue and different shades of grey represent FadD23, Ranked_0, Ranked_1, Ranked_2, Ranked_3, and Ranked_4. (D) The interaction between the N- and C-terminal domains in the substrate-bound state.

Article Snippet: The full AlphaFold v2.0 (AlphaFold2) pipeline was obtained from DeepMind and installed onto a local workstation ( ).

Techniques: Activity Assay