Random Forests Secondary Structure Assignment for Coarse-Grained and All-Atom Protein Systems


Select an Option to see additional information, usage description, and examples.







NOTE: Secondary Structure (SS) assignment is done for amino acids alone, and only the first chain of every frame is read and processed so as to avoid confusing the user. If you must work with many chains, you must submit them separately (otherwise only the first chain will be processed).
Choose PDB File to Upload

[Example: sampleFile.pdb]


Enter (or Copy and Paste) Coordinates* of the Protein in the Space Below





*Note 1: Entered Text Must be in PDB Format.
Note 2: If you do not know what PDB format it, we recommend that you do not use this option at all. If you must use this option, please, refer to this short blog post on PDB Format.


Example: The following is a sample content.
Enter Four-Character* PDB ID:
[Example: 2mqo]




*Note: Entered Characters Must Represent a Valid PDB ID.
Choose PSF* File to Upload

[Example: sampleFile_onlyCA.psf]

Choose DCD* File to Upload

[Example: sampleFile_onlyCA.dcd]




*Note: Only the cordinates of Alpha Carbon atoms (CA alone) are needed regardless of whether you submit all-atom information or not. Therefore, to save bandwidth, please uploaded PSF and DCD files that contain inforation for CA alone. If you do not know how to save PSF and DCD files that contain information of CA atoms alone, please, read this very short tutorial/blog post [ Creating PSF and DCD Files That Contain Only Some Selected Atoms ] we created.



Sample Results
[1] Unfolding of a Native Protein to a Fully-Stretched Form.
[2] Trajectory from a Search for Folding/Melting Temperature of a Protein.
[3] Trajectory from a Monte Carlo Simulation of a Protein.
Be sure to step through the frame-to-frame visualizations of each molecule at the end of each page.


Citation: Salawu, E. O. (2016). RaFoSA: Random forests secondary structure assignment for coarse-grained and all-atom protein systems. Cogent Biology, 2: 1214061. DOI 10.1080/23312025.2016.1214061. [PDF] [Web Server] [Source Code]