The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function
Figure 2
Using structure to predict function.
The protein represented here is PDBid: 2eve. All figures are derived from the Northeast Structural Genomics Consortium structure gallery (http://nmr.cabm.rutgers.edu:9090/gallery/jsp/Gallery.jsp). AstexViewer 2.0 [49] is used for visualization. (A) Superposition of 2eve structure (gray) and of the structure of a homolog (blue, PDBid: 2ar1), using Skan [59]. 2eve hosts three co-crystallized small non-functional ligands (green; ball and stick). Three structurally aligned residues of 2eve and 2ar1 are also shown (red and yellow; ball and stick). (B) Surface residue conservation: Conserved residues (mauve) versus variable residues (cyan). Conservation is calculated as follows: homologs of 2eve are collected using three iterations of PSI-BLAST [15] retaining all homologs with E-value<10−3 and reducing redundancy at 80% sequence identity with CD-HIT [85]. Then, a multiple sequence alignment is created using CLUSTALW [86]. Finally, the multiple sequence alignment is used as input to ConSurf [54], which uses it to calculate residue conservation. (C) Residue conservation within the protein largest cavity (as defined by SCREEN [87]). (D) 2eve surface electrostatic potential (using GRASP2 [59]) (positive in blue, negative in red).