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alphafold colab notebook  (Deepmind Technologies Ltd)

 
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    Structured Review

    Deepmind Technologies Ltd alphafold colab notebook
    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
    Alphafold Colab Notebook, supplied by Deepmind Technologies Ltd, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Screening pertactin-specific antibodies and evaluating competitive epitope recognition by native mass spectrometry"

    Article Title: Screening pertactin-specific antibodies and evaluating competitive epitope recognition by native mass spectrometry

    Journal: Chemical Science

    doi: 10.1039/d5sc09702a

    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and AlphaFold-predicted structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
    Figure Legend Snippet: Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and AlphaFold-predicted structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.

    Techniques Used: Binding Assay, Incubation

    Related Articles

    Protein-Protein interactions:

    Article Title: HBV polymerase recruits the phosphatase PP1 to dephosphorylate HBc-Ser170 to complete encapsidation.
    Article Snippet: .. Prediction of protein-protein interactions with AlphaFold2 Sequences were predicted using AlphaFold Colab (https://colab.research.google.com/github/ deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb) with the default parameters. ..

    Sequencing:

    Article Title: FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins
    Article Snippet: .. In case the predicted structure is not available in the AlphaFold database , the user may carry out the structure predictions for the given sequence in a separate window (Figure ) through AlphaFold Colab provided by DeepMind and Google ( ). ..

    Generated:

    Article Title: Structure of the recombinant RNA polymerase from African Swine Fever Virus.
    Article Snippet: .. Models of all RNAP subunits were generated with AlphaFold228 via AlphaFold Colab (https://colab.research.google.com/ github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb) on Google Colab. ..



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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and <t>AlphaFold-predicted</t> structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.
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    Image Search Results


    Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and AlphaFold-predicted structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.

    Journal: Chemical Science

    Article Title: Screening pertactin-specific antibodies and evaluating competitive epitope recognition by native mass spectrometry

    doi: 10.1039/d5sc09702a

    Figure Lengend Snippet: Binding competition experiments between different pairs of antibodies interacting with the Prn antigen. (A and C) MS1 spectra obtained from incubation of 2B1 (5 µM) with either 1F2 (5 µM) or 1E7 (5 µM) and Prn (5 µM), with deconvoluted spectra shown in the insets on the right. (B and D) Schematic representations of Prn + 2B1-Fab + 1F2-Fab and Prn + 2B1-Fab + 1E7-Fab, respectively, with Prn shaded gray (1DAB), and AlphaFold-predicted structures for 2B1-Fab shaded pink, 1F2-Fab shaded blue and 1E7-Fab shaded purple, all shown as molecular surfaces. The model in 3D displays the potential overlap of 2B1 and 1E7 that would impede simultaneous binding. The presence of high intensity ion peaks centered at m / z 9000 corresponds to complexes containing Prn and two different antibodies that bind to distant epitopes such as 2B1 and 1F2 and demonstrates that two antibodies can simultaneously bind to the Prn antigen. Conversely, simultaneous binding of antibodies that bind to overlapping or proximate epitopes (2B1 and 1E7) is suppressed, resulting in low intensity peaks for the [Ab] 2 ·[Prn] 2 complexes.

    Article Snippet: The folded structures of Fabs of different mAbs were predicted using AlphaFold2 via the publicly available AlphaFold CoLab notebook (DeepMind/EMBL-EBI).

    Techniques: Binding Assay, Incubation