- Calculate the folding nucleus for RNA molecule with known 3D structure including such structures as pseudoknots, tRNAs, hairpins, and ribozymes.
- Calculate the folding nucleus for protein molecule with known 3D.
- Find and understand what elements of structure are limiting in the folding process for different types of RNAs and protein molecules.
- Find experimental Φ-values for about 30 proteins and compare them with our method.
What the user should do:
For the prediction of Φ-values by this server, one should specify RNA or a protein structure for which the prediction is made.
For this purpose, one should specify the corresponding PDB entry in the standard 4-symbol format, for example "1evv" (use "Send" button);
or select and upload local file (in PDB format) (use "Select" button).
For protein or RNA in which more than one chain (or in the case of a protein-RNA complex)
is presented in the PDB file to be used, one should also select which chain should be used
(in the current version, the program simulates unfolding of a single chain protein or RNA molecule).
In addition, there is a possibility to make a prediction for a fragment of the chain
(if, for example, the PDB entry is a crystal of a multi-domain protein, and one wants to simulate
(and predict the Φ-values) for a single domain. To specify the region to be simulated,
one should specify it in the "Region" fields "From" (for example, 120) and "To" (for example, 220) according to the numbering
of the corresponding PDB entry, this means that the server will simulate only the fragment
120-220 of selected chain.
After chain and region selection click "Accept" button or go to Parameters page.
Desired parameters can be modified. The button "Calculate" starts the prediction.
Contacts:
Corresponding Author:
Oxana V. Galzitskaya
Programming:
Leonid B. Pereyaslavets
Web-programming:
Igor V. Sokolovskiy