A constraint logic programming approach to 3D structure determination of large protein complexes

ABSTRACT

The paper describes a novel framework, constructed using constraint logic programming and parallelism, to determine the association between parts of the primary sequence of a protein and α-helices extracted from 3-dimensional low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position, and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

REFERENCES

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INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES

General Terms:
Design, Experimentation

Keywords:
constraint logic programming, protein structure