Supercharge Protein Structure Predictions with Chimerax and Alpha Fold

Supercharge Protein Structure Predictions with Chimerax and Alpha Fold

Table of Contents:

1. Introduction
2. The Speed of Chimerax with Alpha Fold 2.1 Optimization of Chimerax 2.2 The Collaboration with Collab Fold
3. Running Alpha Fold Predictions in Chimerax 3.1 Selecting the Complex 3.2 Pasting Sequences and Options 3.3 Running the Prediction
4. The Output from Colab Fold 4.1 Sequence Alignments 4.2 Sequence Coverage and Sequence Identity 4.3 Predicted Structures
5. Examining the Predicted Structures in Chimerax 5.1 Changing Display Style and Examining Atoms 5.2 Error Plots for Predicted Structures
6. Availability of Alpha Fold in Chimerax

The Speed of Chimerax with Alpha Fold

Protein structure prediction is a crucial aspect of understanding the function and behavior of proteins. In the conventional method, running Alpha Fold predictions could take several hours. However, with the advancements made in Chimerax, this process has been optimized to take just a few minutes. This remarkable improvement in speed has been made possible through collaborations with Collab Fold and by making special optimizations to Chiromarax itself.

Running Alpha Fold Predictions in Chimerax

To demonstrate the speed and efficiency of Alpha Fold in Chimerax, we will focus on a dimeric complex involved in injecting proteins into eukaryotic host cells. To begin the prediction process, the sequences of the two proteins involved are copied and pasted into Chimerax. Users also have the option to use templates from the Protein Data Bank or perform energy minimization on the resulting structure. By clicking the predict button, the prediction process initiates, utilizing the powerful servers of Google Collab.

The Output from Colab Fold

As the prediction process runs, Collab Fold generates some helpful output, which can be examined for better understanding. One such output is the sequence alignments, where approximately 300 sequences matching the input sequences are identified. The sequence coverage plot provides a graphical representation of how different sequences cover the proteins. It shows the coverage of each protein and the sequence identity. A higher sequence coverage and identity indicate a more reliable prediction.

Examining the Predicted Structures in Chimerax

Once the prediction process is complete, the best structures are loaded automatically into Chimerax. These structures are color-coded to represent confidence, with Blue indicating high confidence and yellow and red indicating lesser confidence. Users have the option to further customize the visualization by coloring the two proteins separately. Error plots are available to analyze the predicted errors in the structures and assess their reliability.

Availability of Alpha Fold in Chimerax

The optimization of Chimerax with Alpha Fold is an ongoing process and the latest version of Chimerax, version 1.4, includes these advancements. Users can also access the options discussed in this article in the Chimerax daily builds from July onwards.

In conclusion, the collaboration between Chimerax and Collab Fold has revolutionized protein structure predictions. The significant speed improvements, combined with the intuitive interface of Chimerax, make it a valuable tool for researchers in the field of protein science.