diff --git a/source/_static/structure-prediction/protenix.png b/source/_static/structure-prediction/protenix.png new file mode 100644 index 00000000..e19d031d Binary files /dev/null and b/source/_static/structure-prediction/protenix.png differ diff --git a/source/web-app/structure-prediction/using-structure-prediction.rst b/source/web-app/structure-prediction/using-structure-prediction.rst index 23eb0ac8..b24e140c 100644 --- a/source/web-app/structure-prediction/using-structure-prediction.rst +++ b/source/web-app/structure-prediction/using-structure-prediction.rst @@ -21,6 +21,7 @@ We recommend using: - ESMFold for predictions that must be completed quickly. - MiniFold is a fast single-sequence structure prediction model built on ESM-2, delivering accuracy comparable to ESMFold while reducing inference time by 10–20×. It is designed for rapid prediction of large numbers of protein structures and currently supports single-chain proteins. - RosettaFold-3 is a three-track neural network for protein structure and complex prediction, useful for modeling protein-protein interactions and supporting experimental structure determination. +- Protenix predict the 3D structure of biological molecules including proteins, DNA, RNA, and small molecule ligands, as well as how they interact with each other. Accessing the Structure Prediction tool --------------------------------------- @@ -112,6 +113,20 @@ The **Advanced Options** section contains several parameters: .. image:: /_static/structure-prediction/rosettafold.png :alt: RosettaFold-3 +Using Protenix +----------------- +When using Protenix, you can enter or upload multiple proteins in the input fields provided. + +The **Advanced Options** section contains several parameters: + +- **Number of recycles** Controls how many times the model feeds its predicted structure back into itself for refinement. Higher values improve accuracy but increase computation time. +- **Diffusion Samples** Sets how many independent structure candidates are generated per input. More samples increase the chance of finding the best conformation but proportionally increase runtime. +- **Sampling Steps** Defines the number of denoising steps the diffusion process takes to build each structure. More steps produce more precise, physically valid outputs at the cost of longer inference. +- **Step Scale** Adjusts the sampling temperature, controlling how broadly the model explores structural space. Higher values produce more diverse candidates; lower values give tighter, more consistent results. + +.. image:: /_static/structure-prediction/protenix.png + :alt: Protenix + Visualizing your sequence --------------------------