HELANAL: A Program to Characterize Helix Geometry in Proteins

Bansal, Manju and Kumar, Sandeep and Velavan, R (2000) HELANAL: A Program to Characterize Helix Geometry in Proteins. In: Journal of Biomolecular Structure and Dynamics, 17 (5). pp. 811-819.

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Abstract

A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their $C^{\alpha}$ atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

Item Type: Journal Article Copyright of this article belongs to Adeninepress. Biochemistry and Molecular Biophysics;Computer Applications; Computational Biology Division of Biological Sciences > Molecular Biophysics Unit 03 Oct 2007 03 Feb 2012 10:20 http://eprints.iisc.ernet.in/id/eprint/12047