In this service, we implement two protein structural similarity search methods, SARST and CPSARST.
Besides, three outstanding structural alignment tools, FAST, TM-align and SAMO, are recruited as refinement engines. SE is applied to improve structure-based sequence alignments. We would like to thank these authors for their excellentdevelopments, which greatly move this research field forward.
iSARST allows the user to input many structures at once. Its MPI system will do the similarity searches and structural alignments in a batch mode to rapidly retrieve structural homologs of the query proteins.
SARST is designed for co-linear structural similarity search while CPSARST specifically finds circular permutants. Circular permutation (CP) is a kind of structural rearrangement such that homologous proteins have different locations of termini. It is more and more widely used in protein engineering. Please visit CPDB for detailed information.
How to cite:
Lo WC, Lee CY, Lee CC, Lyu PC: iSARST: an integrated SARST web server for rapid protein structural similarity searches.Nucleic Acids Research 2009, 37(Web Server issue):W545-W551; doi:10.1093/nar/gkp291.
Lo WC, Chang CH, Huang PJ, Lyu PC: Protein structural similarity search by Ramachandran codes.BMC Bioinformatics 2007, 8:307.[Abstract] [PDF]
Lo WC, Lyu PC: CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.Genome Biology 2008, 9:R11.[Abstract] [PDF]