iSARST: an integrated SARST web server for rapid protein structural similarity searches

Abstract

iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARST allows users submitting multiple PDB/SCOP entry IDs or an archive file containing many structures. After scanning the target database using SARST/CPSARST, the ordering of hits are refined with conventional structure alignment tools such as FAST, TM-align and SAMO, which are run in a PC cluster. In this way, iSARST achieves a high running speed while preserving the high precision of refinement engines. The final outputs include tables listing co-linear or circularly permuted homologs of the query proteins and a functional summary of the best hits. Superimposed structures can be examined through an interactive and informative visualization tool. iSARST provides the first batch mode structural comparison web service for both co-linear homologs and circular permutants. It can serve as a rapid annotation system for functionally unknown or hypothetical proteins, which are increasing rapidly in this post-genomics era. The server can be accessed at http://sarst.life.nthu.edu.tw/iSARST/.

Insulin-like growth factor binding protein 7, a member of insulin-like growth factor signal pathway, involved in immune response of small abalone Haliotis diversicolor

“…structure of saIGFBP7 and other IGFBP7 [31]. Phylogenies of protein sequences were estimated with neighbor-joining (NJ) method and MEGA 4.0 software.…”

Molecular cloning and expression of interleukin-1 receptor-associated kinase 4, an important mediator of Toll-like receptor signal pathway, from small abalone Haliotis diversicolor

“…The structural similarity search iSARAT was used (http://sarst.life.nthu. edu.tw/iSARST/) [26]. Phylogenies of protein sequences were estimated using neighbor-joining (NJ) method and MEGA4.0 software.…”

Clostridium thermocellum thermostable lichenase with circular permutations and modifications in the N-terminal region retains its activity and thermostability

“…The program Muscle [28] was used to construct pairwise alignments of amino acid sequences. The circularly permutated lichenase homologs were searched for using iSARST web server [29] and the Blast software in PDB [26]. Potential CP sites in proteins were predicted using the CPred web server [30].…”

“…The circularly permuted lichenase homologs were selected using the program iSARST [29] (option CPSARST [35], Circular Permutation Search Aided by Ramachandran Sequential Transformation) and 3I4I as a template, displaying the maximal homology to LicBM3 and manually tested using the Blast web server. The two templates were selected from the search that met the first condition (PDB ID: 3I4I and 1BYH) and five proteins that met the second one (PDB ID: 1CPN, 1CPM, 1AXK, 1AJK, and 1AJO) ( Table 1).…”