Protein Structure and Function: Application of Bioinformatics Methods - John Rigden 2014
Spatial motifs
Similar methods
Single-point descriptions
The FEATURE program (Bagley and Altman 1995) describes local Structure as a set of properties within concentric shells radiating from a single point. These properties include descriptors for atoms, functional groups, residues, Secondary structure, and simple biophysical characteristics. The radial distribution of properties around functionally interesting points is compared with that around control points, and the statistical significance of any differences is evaluated. However, this approach loses directional information because values are summed over spherical shells. The WebFEATURE server (Liang et al. 2003) (Table 8.3) compares a structure against any of its precomputed patterns representing various site types. Over a hundred patterns are available, though this set is somewhat limited in functional space; many patterns are simply centered on different atoms of the same site type. Precomputed matches are also accessible for specific patterns, individual PDB structures, or protein sets derived from structural Genomics projects.
The S-BLEST web server (Structure-Based Local Environment Search Tool) (Mooney et al. 2005; Peters et al. 2006) (Table 8.3) compares FEATURE-generated patterns—centered on each residue within the query structure—against a database of such patterns containing one pattern per residue from a non-redundant set of PDB structures. The distribution of similarity scores for the query residue provides standardized scores for each specific database residue. The overall match score for a database protein chain is the average of the standardized scores over the top K residues, where K is a user-defined parameter. Chains with scores exceeding a certain threshold are listed along with their GO, EC, and SCOP annotations, alongside sequence-based comparison results. The S-BLEST web server can also be accessed remotely via the molecular graphics interface of UCSF Chimera (Pettersen et al. 2004). The client software can be downloaded from the Life Science Web network (see Table 8.3).
Class="center">Table 8.3. Web servers utilizing similar approaches
Name and URL |
Server function |
Downloads |
S-BLEST www.sblest.org |
Compares residue-centered configurations in the query structure against a non-redundant set of PDB structures, returning a list of the most similar chains and their annotations |
S-BLEST can also be used remotely with visualization in UCSF Chimera (www.cgl.ucsf.edu/chimera). Chimera plugins for Windows, Linux, and Mac OSX can be downloaded at: www.lifescienceweb.org |
SiteEngine bioinfo3d.cs.tau.ac.il/SiteEngine |
Compares a Ligand-bound binding site in a structure against the entire surface of another structure |
A Linux executable is available strictly for non-commercial use |
WebFEATURE feature.stanford.edu/webfeature |
Compares the query structure against precalculated point-centered configurations representing several dozen functional sites |
The source code for the FEATURE program can be downloaded at: simtk.org/home/feature |
Last update: 06/08/2026
Editorial and Educational Adaptation: This material has been compiled based on the primary/original source text. The project team performed an editorial review, corrected technical inaccuracies, structured sections, and adapted the content for an educational format.
What was processed:
- elimination of formatting defects (OCR errors, structural breaks, corrupted characters);
- editorial organization of content;
- standardization of terminology in accordance with academic sources;
- verification of factual statements against the original source text.
All mentions of the author, publication year, and origin of the primary text have been preserved in accordance with the source.