Software

Surface Racer©

Surface Racer calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside. The output includes the surface parameters for each residue in addition to those for individual atoms.

The program runs on most common computer platforms, as specified below.

This program should be referenced as:

Tsodikov, O. V., Record, M. T. Jr. and Sergeev, Y. V. (2002). A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comput. Chem., 23, 600-609.

The following programs are provided free of charge only for academic use. By downloading these programs you implicitly agree that they will be used exclusively in academic research.

Program Installation (for all operating systems): place the binary file and the radii.txt file in the same directory as the pdb file (no hydrogens or NMR ensembles allowed). The program is ready to run. For more important details see the readme file in the distribution.

The author claims no responsibility for any problems associated with the use of the software downoaded from this webpage.

Thanks:
- to Emre Brooks and Borries Demeler at the University of Texas at San Antonio for an important code improvement, incorporated into version 5.0.

- to Piotr Sliz and Ben McClure at Harvard Medical School for compiling the code for OS X and for providing additional support for this software through a fantastic computational resource for structural biologists, the SBGrid Consortium.

ITC Planning and Simulation Tool©

The following ITC planning tool (in a MS Excel format) is provided free of charge for academic use. Choose the appropriate spreadsheet for your titration method by clicking on the Perfusion or the Simple tab on the bottom. Choose Perfusion when the sample cell is filled up completely at the beginning of the titration. Choose Simple when the sample cell fills up during a titration. The input parameters are set at desired values. Injection volumes can be set independently for each titration. The titration graph and the heat values are then calculated automatically. The titration is simulated for a 1:1 binding equilibrium.

Please, cite this tool as follows:
Biswas, T. and Tsodikov, O.V. (2010) An easy-to-use tool for planning and modeling a calorimetric titration. Anal. Biochem., 406, 91-93.

page last modified: April 18 2013     

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