Structure Analysis

Toolkit


Perform Key operations on a 3D structure.


Secondary Structure, Accessibility, Hydrogen bonds and Motifs.

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Procheck

The Procheck suite calculates various core data including bond angles and lengths, torsion angles as well as properties such as secondary structure assignments, using the method described by Kabsch & Sander.

Procheck can also assess the quality of a 3D structure, a functionality for which it is best known, by comparing properties for an individual structure to those typically found for a basket of well determined structures.

Naccess

This is a text-book implementation of the Lee and Richard accessibility calculation. This robust algorithm generated both atom and residue accessibilities which are expressed as both absolute and relative values.

HBplus

Hydrogen bond calculations are very important. This implementation uses both distance and angle constraints and is used as the default input to Ligplot+. For more information see the following publication.

I.K. McDonald and J.M. Thornton (1994) JMB 238:777-793
"Satisfying Hydrogen Bonding Potential in Proteins"


Promotif


This convenient program takes secondary structure output and calculates a set of structural motifs. The program provides information about the following structural features:

  1. secondary structure

  2. beta and gamma turns

  3. helical geometry and interactions

  4. beta strands and beta sheet topology

  5. beta bulges

  6. beta hairpins

  7. beta-alpha-beta units

  8. psi-loops

  9. main-chain hydrogen bonding patterns


Beta Turn Classification

Helical Nets

Bulge Classification

Hera Plot

Main Chain H bond diagram

Hairpin Classification

Promotif - Sample Graphical

Topology Maker


Using the Hera output, we can use Topology Maker to simplify this down into a topology diagram like this one. Convenient!