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JournalSelect: Stochastic Gradient Descent Prediction of the Most Suitable Journals for a New Manuscript
RaFoSA: Random Forests Secondary Structure Assignment for Coarse-Grained and All-Atom Protein Systems
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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.



User Guide (Concise Version)
HTML: [Open Here]
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PDF:     [Download/View PDF in a New Tab]


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.



About ProSSA

We have developed ProSSA for (Hydrogen-Bond-Independent) Proteins' Secondary Structure Assignment). ProSSA requires only the coordinates of CA atoms and works independent of hydrogen-bond patterns of the protein’s residues. Therefore, ProSSA can be used for secondary structure (SS) assignment to protein's amino acids following coarse-grained (CG) molecular dynamics (MD) simulations of protein molecules or whenever all-atom information is lacking. ProSSA provides a reliable and accurate solution to an important problem in protein science. (Until we developed ProSSA, the problem had been the lack of a "reliable and accurate" method for SS assignment to protein's amino acids whenever all-atom information as well as hydrogen-bond information is not available).

ProSSA is based on deep learning and an in-house implementation of a novel and reliable algorithm for automatic SS assignment using the coordinates of alpha carbon (CAC) atoms alone.

At this point we must emphasize that SS assignment by ProSSA is different from (and is much more rigorous than) SS prediction from amino acids sequence. For example, while SS assignment by ProSSA can differentiate between two different frames from an MD simulation's trajectory, SS prediction from amino acids sequence cannot. Such additional information that ProSSA provides even following CG MD simulations (and regardless of whether hydrogen-bond information and all-atom information are available or not) are of great importance to structural, molecular, and computational biology/biologist. Please, see the results of some examples of such frame-to-frame SS assignment on these pages. [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. We believe you will like it.

We have compared the results from ProSSA to those from Dictionary of Protein Secondary Structure (DSSP1 as well as its variants, which is widely seen as the gold standard for automatic SS assignment) and STRIDE2 (which is shipped with Visual Molecular Dynamics). Requiring only CAC (i.e. not requiring all-atom and hydrogen-bonding information), ProSSA achieves an unprecedented agreement of 96% (and 94%) with DSSP (and STRIDE) that require all-atom and hydrogen-bonding information.

Selected references
1 Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983).
2 Heinig, M. & Frishman, D. STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res. 32, 500–502 (2004).



Address for Correspondence
Email: tools@bioinformatics.center