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Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates
Author(s) -
Hermans Jan,
Ferro Dino
Publication year - 1971
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360100704
Subject(s) - representation (politics) , basis (linear algebra) , computation , notation , dihedral angle , computer program , modular design , tree (set theory) , computer science , theoretical computer science , computational science , molecule , chemistry , algorithm , programming language , geometry , mathematics , arithmetic , combinatorics , hydrogen bond , organic chemistry , politics , political science , law
Abstract The concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.