FEEDBACK ALGORITHM AND WEB-SERVER FOR PROTEIN STRUCTURE ALIGNMENT

We have developed a feedback algorithm for protein structure alignment between two protein backbones. A web portal implementing this method has been constructed and is freely available for use at http://fpsa.cs.uno.edu/ with a mirror site at http://fpsa.cs.panam.edu/FPSA/. We compare our algorithm with three other, commonly used methods: CE, DaliLite and SSM. The results show that in most cases our algorithm outputs a larger number of aligned positions when the (C_α) RMSD is comparable. Also, in many cases where the number of aligned positions is larger or comparable, our learning method is able to achieve a smaller (C_α) RMSD than the other methods tested. This trend of larger number of aligned positions and smaller (C_α) RMSD is observed more frequently in cases where the similarity between protein structures is weak.