Fragment Finder: a web-based software to identify similar three-dimensional structural motif

Abstract

FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles (phi and ). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling. The engine has facilities to view the resultant superposed or individual 3D structure(s) on the client machine. The proposed web server is made freely accessible at the following URL: http://cluster.physics.iisc.ernet.in/ff/ or http://144.16.71.148/ff/.

Figure 1

The top panel of the output page displays the main-chain conformation angles for the input fragment (residues 2–9 from the PDB-ID code 1UNE). The bottom panel shows the output of the matched structural fragments (only PDB-IDs) found in 25% non-homologous protein chains.

Figure 2

The output page depicts the superposition (top middle panel) of the 13 hits listed at the bottom of Figure 1. The left panel displays the location of the input fragment (ribbon colored green) with respect to the entire molecule (backbone trace). The right bottom panel displays the superposition (using the program STAMP) of all the 13 hits found by the search engine. This panel can be invoked by clicking the option ‘Display all the structures’.