STRUCTURAL ANALYSIS TOOLKIT

Perform a variety of key operations on 3D structures.

Analyse Secondary Structure, Topology, Protein Quality, Loop classification, Accessibility, Hydrogen bonds and Motifs.


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Procheck

Calculates core data including bond angles and lengths, torsion angles as well as hydrogen bonds and secondary structure assignments. 

Procheck assesses the quality of a 3D structure (the functionality for which it is best known) by comparing properties of an individual structure to statistics generated from known high quality structures.


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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.

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Hera

Automatically calculates and draws a 2D representation of all the hydrogen bonding in a protein based on secondary structure data calculated by Promotif


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HBplus

Hydrogen bonds depend on both distance and angle. This was the first program to apply both constraints. HBPlus is used as the default input to Ligplot+. For more information on HBplus see the following publication.

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

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Topology

A simplification of the Hera output showing more figuratively the layout of protein secondary structure elements.


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Promotif

Takes secondary structure output, calculates a set of structural features:

  • beta and gamma turns

  • helical geometry and interactions

  • beta strands and sheet topology

  • beta bulges

  • beta hairpins

  • beta-alpha-beta units

  • psi-loops

  • main-chain hydrogen bonding patterns