The integrated Service of Structural similarity search Aided by Ramachandran Sequential Transformation


In this iSARST service, we have implemented two protein structural similarity search methods, i.e. SARST and CPSARST. There methods were developed by our group. Besides, we currently recruit two very accurate structural alignment tools, FAST and TM-align, and an order-independent alignment method, SAMO, as the refinement engines. To improve the quality of structure-based sequence alignments, SE is applied.

We would like to thank these authors for their excellent developments, which have greatly moved this research field forward and saved much time and efforts for those scientists who need to perform structual comparisons very frequently.

This service is running on a PC-cluster, users can input a lot of query structures at the same time. Our multi-processor implementation system will run SARST/CPSARST and FAST/TM-align in a batch mode to rapidly retrieve structural homologs of the query proteins.

SARST is designed for common (or, co-linear) structural similarity search while CPSARST specifically retrieves circular permutants from the target database. Circular permutation is a kind of structural rearrangement such that the original N- and C-termini seems to be linked and new termini were created elsewhere. It is more and more widely used in protein engineering. Please visit our CPDB for detailed information.

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]

Lo WC, Lee CC, Lee CY, Lyu PC: CPDB: a database of circular permutation in proteins
Nucleic Acids Research 2008, doi:10.1093/nar/gkn679 (Database Issue). [Abstract] [PDF]

Zhu J, Weng Z: FAST: a novel protein structure alignment algorithm.
Proteins 2005, 58:618-627. [Abstract] [PDF]

Zhang Y, Skolnick J: TM-align: a protein structure alignment algorithm based on the TM-score.
Nucleic Acids Research 2005, 33:2302. [Abstract] [PDF]

Chen L, Wu LY, Wang Y, Zhang S, Zhang XS: Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
BMC Structural Biology 2006, 6:18. [Abstract] [PDF]

Tai CH, Vincent JJ, Kim C, Lee B: SE: an algorithm for deriving sequence alignment from a pair of superimposed structures.
BMC Bioinformatics 2009, 10(Suppl 1):S4. [Abstract] [PDF]