the automatic assignment of protein secondary structure from three dimensional coordinates is an essentialstep in the characterization of protein structure.although, the recognition of secondary structures suchas alpha-helices and beta-sheets seem straightforward, but there are many different definitions, eachregarding different criteria. we have developed a newalgorithm for protein helix assig...

The automatic assignment of protein secondary structure from three dimensional coordinates is an essential step in the characterization of protein structure. <span style="font...

We present a new automatic algorithm, named VoTAP (Voronoï Tessellation Assignment Procedure), which assigns secondary structures of a polypeptide chain using the list of alpha-carbon coordinates. This program uses three-dimensional Voronoï tessellation. This geometrical tool associates with each amino acid a Voronoï polyhedron, the faces of which unambiguously define contacts between residues....

We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently ...

We present a new automatic algorithm, named VoTAP (Voronoı̈ Tessellation Assignment Procedure), which assigns secondary structures of a polypeptide chainusing the list of -carbon coordinates. This program uses three-dimensional Voronoı̈ tessellation. This geometrical tool associateswith each amino acid aVoronoı̈ polyhedron, the faces of which unambiguously define contacts between residues. Thanks ...

http://www.hgmp.mrc.ac.uk/Registered/Option/stride.html Protein Secondary Structure Assignment and Prediction Defining SS features Dihedral angles, alpha helix, beta stand (Hydrogen bonds) Assigned manually by crystallographers or Automatic DSSP (Kabsch & Sander,1983) STRIDE (Frishman & Argos, 1995) Continuum PCE: Protein Continuum Electrostatics (Andersen et al.) http://bioserv.rpbs.jussieu.fr...

MOTIVATION The secondary structure is a key element of architectural organization in proteins. Accurate assignment of the secondary structure elements (SSE) (helix, strand, coil) is an essential step for the analysis and modelling of protein structure. Various methods have been proposed to assign secondary structure. Comparative studies of their results have shown some of their drawbacks, point...

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algori...