Welcome to DeepFold-PLM, our state-of-the-art protein structure prediction platform. This tutorial will guide you through the process of using our service, from submitting protein sequences to analyzing the predicted structures.
Our web application follows a straightforward workflow that makes it easy to predict protein structures. Follow these steps to get started with DeepFold-PLM.
Create an account or sign in to access the full functionality of our platform. While browsing is available to all visitors, you'll need an account to submit prediction jobs and save your results.
The home page provides quick access to all features. From here, you can start a new prediction, view your job history, or access the tutorial and paper sections.
Enter your protein sequence in the input field on the home page, then click 'Continue and preview job' to initiate the prediction process. More details on this step are provided in the next section.
After submission, you can track your job's progress in the History section. The status will update in real-time as shown below:
Once the job is completed, click on it to view the results. You'll have access to various analysis tools that help you interpret the predicted structure.
Let's walk through the process of submitting a protein structure prediction job step by step.
After entering your protein sequence, click the "Continue and preview job" button to submit your prediction request. The system will validate your input and create a new job.
Once your job is submitted, you can track its progress in the History section. Completed jobs will have a "View Analysis Page" button that takes you to the results dashboard.
Once your prediction job is complete, the Analysis page provides comprehensive insights into your protein's structure. The following sections explain the various analysis tools available.
The Single Sequence Analysis provides detailed information about your protein's properties based on the primary sequence. This includes Relative Solvent Accessibility (RSA) values and secondary structure predictions for each residue.
The visualization above shows:
The 3D structure viewer allows you to explore your protein's predicted structure in a fully interactive environment. Alongside it, the distogram visualization provides insights into residue-residue distances.
The Ramachandran plot is a valuable tool for assessing the quality of predicted protein structures. It visualizes the distribution of backbone dihedral angles (φ and ψ) for all residues in the protein.
The Ramachandran plot helps validate the quality of the predicted structure:
The MSA depth visualization shows how many aligned sequences cover each position in your query protein. This information is crucial for understanding the evolutionary conservation and reliability of the predicted structure.
Key aspects of the MSA depth visualization: