Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis
- 1 January 1989
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 6 (1) , 46-60
- https://doi.org/10.1002/prot.340060105
Abstract
We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinated of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.Keywords
This publication has 22 references indexed in Scilit:
- Conformational and Helicoidal Analysis of 30 PS of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: “Curves”, Dials and WindowsJournal of Biomolecular Structure and Dynamics, 1989
- Defining the Structure of Irregular Nucleic Acids: Conventions and PrinciplesJournal of Biomolecular Structure and Dynamics, 1989
- Definitions and Nomenclature of Nucleic Acid Structure ParametersJournal of Biomolecular Structure and Dynamics, 1989
- The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic AcidsJournal of Biomolecular Structure and Dynamics, 1988
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983
- The Anatomy and Taxonomy of Protein StructurePublished by Elsevier ,1981
- Specific recognition in the tertiary structure of β-sheets of proteinsJournal of Molecular Biology, 1980
- Differential Geometry and Polymer Conformation. 1. Comparison of Protein Conformations1a,bMacromolecules, 1978
- Automatic identification of secondary structure in globular proteinsJournal of Molecular Biology, 1977
- Stereochemical Criteria for Polypeptide and Protein Chain ConformationsBiophysical Journal, 1965