Preprint Hypothesis Version 1 This version is not peer-reviewed

A Local Spherical Coordinate System Approach to Protein 3D Structure Description

Wei Li * ORCID logo
Version 1 : Received: 12 January 2020 / Approved: 12 January 2020 / Online: 12 January 2020 (17:23:18 CET)

How to cite: Li, W. A Local Spherical Coordinate System Approach to Protein 3D Structure Description. Preprints 2020, 2020010133 (doi: 10.20944/preprints202001.0133.v1). Li, W. A Local Spherical Coordinate System Approach to Protein 3D Structure Description. Preprints 2020, 2020010133 (doi: 10.20944/preprints202001.0133.v1).

Abstract

To date, Cartesian (x, y, z) coordinate system (CCS) has been the default approach to geometrically specify atomic spatial positions in protein structures since the launch of Protein Data Bank (PDB) in 1971. To this end, this paper proposes a local spherical coordinate system (SCS) approach as an alternative to the default approach and a previously reported global SCS approach. The local SCS approach here requires only two parameters (θ and φ), instead of x, y and z as required by the default CCS approach. Essentially, CCS and SCS are like the two sides of one coin, i.e., geometric coordinate system for three-dimensional position specification. Therefore, this paper furthermore argues that it is time to flip the coin over, and have a look at the other side of the coin, e.g., the local SCS approach, which possesses an intrinsically lower degree of descriptional complexity than that of the default CCS approach, and constitutes a potentially useful alternative perspective for all protein structural research field.

Subject Areas

Cartesian Coordinate System; Spherical Coordinate System; Equilibrium Atomic Bond Length; Protein Structure Description; Protein Structure Tree-decomposition

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