A Constraint Logic Programming approach to associate 1D and 3D structural components for large protein complexes

Authors:
Alessandro Dal Palu;Enrico Pontelli;Jing He;Yonggang Lu
Affiliations:
Facolta di Scienze MM FF e NN, Dipartimento di Matematica, Universita di Parma, Parco Area delle Scienze 53/A, 43100 Parma, Italy.;Computer Science Department, New Mexico State University, BOX 30001 MSC CS, Las Cruces, NM, 88003, USA.;Computer Science Department, New Mexico State University, BOX 30001 MSC CS, Las Cruces, NM, 88003, USA.;Computer Science Department, New Mexico State University, BOX 30001 MSC CS, Las Cruces, NM, 88003, USA
Venue:
International Journal of Data Mining and Bioinformatics
Year:
2007

Citing 3
Cited 1

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Abstract

The paper describes a novel framework, constructed usingConstraint Logic Programming (CLP) and parallelism, to determinethe association between parts of the primary sequence of a proteinand α-helices extracted from 3D low-resolution descriptionsof large protein complexes. The association is determined byextracting constraints from the 3D information, regarding length,relative position and connectivity of helices, and solving theseconstraints with the guidance of a secondary structure predictionalgorithm. Parallelism is employed to enhance performance on largeproteins. The framework provides a fast, inexpensive alternative todetermine the exact tertiary structure of unknown proteins.