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| Volume Area Dihedral Angle Reporter ： ウィキペディア英語版 |
Volume Area Dihedral Angle Reporter
Volume, Area, Dihedral Angle Reporter (VADAR) is a freely available protein structure validation web server that was developed as a collaboration between Dr. Brian Sykes and Dr. David Wishart at the University of Alberta.〔 VADAR consists of >15 different algorithms and programs for assessing and validating peptide and protein structures from their PDB coordinate data. VADAR is capable of determining secondary structure (using 3 different algorithms), identifying and classifying 6 different types of beta turns, determining and calculating the strength of C=O -- N-H hydrogen bonds, calculating residue-specific accessible surface areas (ASA), calculating residue volumes, determining backbone and side chain torsion angles (phi, psi, omega and chi angles), assessing local structure quality (through numerous quality indices), evaluating global structure quality and identifying residue “outliers” (residues with unusual structural features). The results have been validated through extensive comparison to published data and careful visual inspection. VADAR produces both text and graphical output with most of the quantitative data presented in easily viewed tables. In particular, VADAR’s output is presented in a vertical, tabular format with most of the sequence data, residue numbering and any other calculated property or feature presented from top to bottom, rather than from left to right.
==Identification of Secondary Structure==
VADAR identifies and assigns protein secondary structure using 3 different algorithms. These three methods are then combined to create a consensus secondary structure assignment. Only 3 types of secondary structure are identified: Helices are indicated with an "H", beta-strands are indicated with a "B" and coil or unstructured regions are identified with a "C". Secondary structure assignments for each residue are listed under the column labeled SCND STRUC. The first secondary structure identification method (which appears in column 1) uses a geometric masking approach that was first described by Richards and Kundrot with slight modifications. The second method (which appears in column 2) uses backbone dihedral angles to identify secondary structure elements in a manner initially described by Levitt and Greer as well as Chou and Fasman. The third secondary structure identification method uses hydrogen bonding patterns (in association with measured dihedral angles) to identify helices, beta strands and coil regions. This third method is somewhat similar to the method originally described by Kabsch and Sander. The net result or consensus secondary structure is a weighted combination of each of the three methods. VADAR’s method of secondary structure identification generally identifies a higher fraction of secondary structure elements than the DSSP algorithm (64% helices and beta strands for VADAR versus 51% helices and beta strands for DSSP). In particular, VADAR’s secondary structure assignments appear to agree more closely with secondary structures identified by visual inspection (i.e. author assignments), by STRIDE (another secondary structure assignment algorithm) or via independent methods (i.e. NMR-based NOE methods).
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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