biology

Volume Area Dihedral Angle Reporter

Volume Area Dihedral Angle Reporter is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Volume Area Dihedral Angle Reporter rather than just read about it. In short: 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.

Key takeaways

Volume Area Dihedral Angle Reporter belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Volume Area Dihedral Angle Reporter to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Volume Area Dihedral Angle Reporter from memory before moving on to harder problems.

Reference excerpt

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 over 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 three different algorithms), identifying and classifying six 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).

Calculation of Accessible Surface Area Accessible surface areas is a measure of the solvent exposure of individual atoms or residues (measured in square Angstroms). It corresponds to the surface area of an atom (or residue) that a water molecule can access or touch. In VADAR, the accessible surface areas (ASA) for each residue is presented under two different column headers: RES ASA (residue ASA) and FRAC ASA (fractional ASA). The data listed under the RES ASA column refers to the “residue accessible surface areas” as measured in square Angstroms. The data listed under the FRAC ASA column refers to the fractional residue accessible surface areas (a value ranging from 0 to 1.0). Exposed, exterior, random coil or hydrophilic residues typically have a large fractional accessible surface areas (>0.5), while hydrophobic, beta sheet or interior residues have a small fractional accessible surface areas (<0.2). The fractional accessible surface areas is calculated by dividing a given residue’s observed accessible surface areas by the calculated accessible surface areas for that residue in an extended Gly-Xaa-Gly tripeptide (where Xaa is the residue of interest). VADAR reports accessible surface are values both for the entire amino acid residue and for the amino acid side chains. The accessible surface areas is also calculated for charged atoms (N, O), polar (N, O, S) atoms and for non-polar atoms (C). This information can be used to calculate charged, polar and non-polar surface area. Accessible surface areas measurements/estimates are particularly useful in protein structure assessment, protein structure validation and thermodynamic calculations. The values calculated for accessible surface areas (ASA) depend critically on the selection or choice of atomic or Van der Waals radii. Different methods and different authors have advocated the use of different atomic radii. As a result, VADAR provides several choices for atomic or Van der Waals radii.

Calculation of Backbone and Side Chain Torsion Angles Protein torsion angles are calculated for phi, psi, omega (which corresponds to the peptide bond) and chi1 (the first side chain torsion angle) using standard IUPAC definitions. These values are listed under four different column headers: PHI, PSI, OMEGA and CHI1. All torsion angles are reported in degrees. Torsion angles are a very useful indicator of the stereochemistry and the stereochemical quality of a protein structure, with most high-quality proteins exhibiting a relatively tight clustering of phi/psi angles and relatively little deviation in the omega angles.

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Worked examples

Example 1 — a first encounter with Volume Area Dihedral Angle Reporter

Start with the simplest possible case. Write down what Volume Area Dihedral Angle Reporter claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Volume Area Dihedral Angle Reporter before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Volume Area Dihedral Angle Reporter ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Volume Area Dihedral Angle Reporter

In research: Volume Area Dihedral Angle Reporter appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Volume Area Dihedral Angle Reporter in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Volume Area Dihedral Angle Reporter is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein structure databases, so understanding it makes those chapters shorter.
In everyday life: Look for Volume Area Dihedral Angle Reporter outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Volume Area Dihedral Angle Reporter in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Volume Area Dihedral Angle Reporter means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Volume Area Dihedral Angle Reporter out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Volume Area Dihedral Angle Reporter in simple terms?

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.

Why does Volume Area Dihedral Angle Reporter matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Volume Area Dihedral Angle Reporter?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Volume Area Dihedral Angle Reporter.