ProtSA: calculation of sequence specific protein solvent accessibilities in the unfolded ensemble
Welcome to the ProtSA web application. ProtSA will calculate, for your protein of interest, the average solvent accessible surface area (SASA) of each atom and residue in the unfolded-state ensemble. All you need to provide is the sequence of your protein. The accessibilities calculated by ProtSA for any residue are strongly sequence dependent and may be useful to understand mutational studies in proteins and to improve parameterizations of protein folding energetics.
In addition, if you provide a structural model (a PDB code, or your own file in PDB format), folded SASA and differences between the folded and unfolded SASA, per atom and per residue, will be calculated. Color-coded sequences summarize the results, and the structural model provided is returned with the B-factor column containing the ratio between the residue folded SASA and its unfolded SASA, allowing a straightforward three-dimensional visualization of exposure changes associated to protein folding.
The results will be e-mailed to the address you provide. You can find a more detailed explanation of this service in a separate page. The description of the method used for the calculation appears in the main reference (Bernadó et al. (2006)), though this server has some modifications, which are explained in the information page (see also the paper describing this server: Estrada et al. (2009)). Next to each field of the form, there is an information icon which leads you to the description of this field, below in this same page.
If you want to apply ProtSA to a set of sequences, please contact us (J. Sancho, contact details) to do those calculations off-line. Future versions of ProtSA will manage such computationally demanding calculations.