SABA (secondary structure assignment program based on only alpha carbons): a novel pseudo center geometrical criterion for accurate assignment of protein secondary structures

Knowledge-based protein secondary structure assignment.

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 ...

Secondary structure assignment.

Protein secondary structure assignment through Voronoï tessellation.

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....

Protein Secondary Structure Assignment Through Voronoı̈ Tessellation

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 ...

Protein Secondary Structure Assignment and Prediction

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...