Bluues  Electrostatic properties of proteins based on generalized Born radii 
Quick Help and References 
Description 
The PoissonBoltzmann (PB) equation and its linear approximation have been widely used to
describe biomolecular electrostatics [3]. Generalized Born (GB) models offer a convenient computational
approximation for the more fundamental approach based on the PoissonBoltzmann equation, and allows
estimation of pairwise contributions to electrostatic effects in the molecular context.
This server concerns the implementation of the most common features of the electrostatic properties of proteins. The server first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. The output of the server can be summarized as follows:
The results obtained are comparable to those obtained using stateoftheart PoissonBoltzmann solvers but this method but this method may be more efficient because it depends on the accuracy required and on the size of the system. Moreover, the algorithm produces Born radii which allow calculation of pairwise interactions, an information not directly available in the PoissonBoltzmann based methods. The server is designed for easy usage with output in the form of easy comprehensible graphs, sorted tables and molecular viewers in JMol. A more detailed description of the output will be provided later. 

EMail address 
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recommend using an email.

Job tag for structure 
An optional title for your submission. This will appear in the header
of the output. We suggest you select one, especially if sending
multiple queries, as they may be completed in a different order.

Structure 
This is where you must provide information about your structure. There are 3 possibilities for providing the structure:


Generalized Born (GB) radii and Potential at atomic surface 
Both GB radii and Potential at atomic surface are executed by default since they are the most
basic type of computation and they are efficient.
The computation of GB radii is performed by surface integrals. GB models provide efficient and accurate calculations for the electrostatic effects of the solvent [57]. The radii allow the calculation of interaction energy between any two charges and from a purely geometric point of view they give a measure of the atom depth in the structure. The Potential at atomic surface is computed as the energy of interaction all atoms of the molecule with a unit test charge with a generalized Born radius equal to half the solvent probe radius, (i.e. 0.7Å by default). The potential is greatly influenced by partial or net charges on the molecule, but also by molecular shape. For more detailed descriptions see the bluues methods paper in the reference section. 
pka shifts 
This option will generate pHdependent properties such as total charge, pHdependent free energy of folding, and pKa of ionizable
groups as well as titration curves for each titratable residue. Here we follow the approach of
[8] with the advantage that the Green's functions are obtained directly within the
GB approach whereas they require multiple calculations in the PB approach.In bluues methods paper(see reference section) the results were compared with
the commonly used Propka2.0 [10] showing comparable (or better on the chosen dataset) performances.

Surface area 
The solvent accessible surface area (i.e. the surface accessible by the center of a solvent probe sphere) is computed based on a grid mapping of all atoms. This is provided for completeness and/or further use. GB radii are computed based on this surface.




Using the surface area and pKa options: 

Protein information 

Available files 
Default options:
If Surface Area clicked:
If pKa clicked:

Visualisation 
The molecular view and its surface potential is displayed using the JMOL visualisation tool. 