SAAFEC (Single Amino Acid Folding free Energy Changes) is an approach for calculating folding free energy changes caused by missense mutations. The method is based on weighted MM-PBSA method with weight coefficients optimized against experimental data from the ProTherm database. Furthermore, the prediction formula is extended to include various biophysical terms to enhance the performance.
A quick overview of how everything works:
- A membrane protein coordinate file is needed (PDB file format only). The user needs to specify the location and type of mutation.
- The uploaded protein is then 'fixed' using an algorithm in order to add missing residues or heavy atoms. The mutation is then introduced in the location specified by the user using the SCAP software. Two files are created; one for the wild type and one for the mutant type.
- The protein structures then undergo a minimization using the NAMD software (3000 steps).
- Various energies calculations are then performed on the minimized struturess.
If the usage of the server results in scientific publication, please, cite the following paper: "Getov, I.; Petukh, M.; Alexov, E. SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach. Int. J. Mol. Sci. 2016, 17, 512. doi: 10.3390/ijms17040512."
SAAFEC is running on Clemson University's Palmetto Supercomputer cluster. We would like to thank the Palmetto team for hosting this service. We also would like to acknowledge NIH-Grant# R01 GM093937 for supporting this work.