GETAREA

Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies and Their Gradients for Macromolecules

Surendra Negi, Hongyao Zhu, Robert Fraczkiewicz, Werner Braun

Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555


Quite often a biomolecular researcher wants to quickly calculate solvent accessible surface area or solvation energy of, for example, a protein molecule but does not have time/resources/skills/will to find and install an appropriate software. GETAREA, our efficient method of calculating the solvent accesible surface area [1,2] implemented in program FANTOM, can be directly accessed through this form. An on-line manual is available. Atomic coordinates should be supplied in PDB format. Please cite reference [1] in publications that use our service. Comments are welcome, please mail them to ssnegiATutmb.edu or webraunATutmb.edu .
                                  


y or n, Default is n
For information purpose only
                                                                         

ADVANCED OPTIONS:

This is a default database of atomic radii and atomic solvation parameters (ASP). By changing its entries you can calculate surface areas for only specific atom types or switch the program to calculate solvation energies with different ASP sets. Please consult the manual for more info. Calculation of solvent accessible surface area of non-hydrogen atoms (for which all ASP=1.0) is the default. Please add one empty line after you add ASP values.

This is a default library that assigns names of protein atoms to their respective types (the fifth column of ASP database above). Atom name entries follow IUPAC (Pure & Appl. Chem. 70, 117, 1998) plus all PDB violations of these rules. It should suffice for most of proteins. By changing library and ASP database entries you can calculate surface areas and/or solvation energies of molecules different than proteins, e.g. carbohydrates (see manual). Please add one empty line after you add atom types values.



Please make sure that you are using standard amino acids and atoms name. A complete list is available here : HELP
Using multipe pdb files!

Users can use Getarea_Remote.pl program to submit multiple PDB files to getarea server. Click this link to download Getarea_Remote.pl program.

Disclaimer:

This service is provided freely to the scientific community for the purpose of scientific research. There is no warranty for the service, either expressed or implied. The entire risk as to the quality and performance of the service is with the user. In no event will Sealy Center for Structural Biology be liable for any damages, including any general, special or consequential damages arising out of the use, misuse, or inability to use of this service.

References:

  1. Fraczkiewicz, R. and Braun, W. (1998) "Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients for Macromolecules" J. Comp. Chem., 19, 319-333.
  2. Fraczkiewicz, R. and Braun, W. "A New Efficient Algorithm for Calculating Solvent Accessible Surface Areas of Macromolecules" presented at the Third Electronic Computational Chemistry Conference; Northern Illinois University; November 1996; World Wide Web.


Last modified on Tue Friday April 17, 3:00 PM 2015 by Surendra Negi. For more information visit: http://curie.utmb.edu

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