Applying constraint programming to protein structure determination

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

14 Citations (Scopus)

Abstract

In this paper, we propose a constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA (“Dynamics algorithm for NMR applications” [1]) an existing commercial application based on simulated annealing. For our test case, computation time for DYANA was more than six hours, whereas the method we propose produced similar results in 8 minutes, so we show that the application of Constraint Programming (CP) technology can greatly reduce computation time. This is a major advantage because this NMR technique generally demands multiple runs of structural computation.

Original languageEnglish
Title of host publicationPrinciples and Practice of Constraint Programming – CP 1999 - 5th International Conference, CP 1999, Proceedings
EditorsJoxan Jaffar
PublisherSpringer Verlag
Pages289-302
Number of pages14
ISBN (Print)3540666265, 9783540666264
DOIs
Publication statusPublished - 1999
Event5th International Conference on Principles and Practice of Constraint Programming, CP 1999 - Alexandria, United States
Duration: 11 Oct 199914 Oct 1999

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume1713
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference5th International Conference on Principles and Practice of Constraint Programming, CP 1999
Country/TerritoryUnited States
CityAlexandria
Period11/10/9914/10/99

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