Protein structure determination via an efficient geometric build-up algorithm

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dc.date.accessioned 2010-06-08T19:37:15Z
dc.date.available 2010-06-08T19:37:15Z
dc.date.issued 2010-05-17
dc.identifier http://dx.doi.org/10.1186/1472-6807-10-S1-S7
dc.identifier.uri http://hdl.handle.net/2271/833
dc.description.abstract Abstract Background A protein structure can be determined by solving a so-called distance geometry problem whenever a set of inter-atomic distances is available and sufficient. However, the problem is intractable in general and has proved to be a NP hard problem. An updated geometric build-up algorithm (UGB) has been developed recently that controls numerical errors and is efficient in protein structure determination for cases where only sparse exact distance data is available. In this paper, the UGB method has been improved and revised with aims at solving distance geometry problems more efficiently and effectively. Methods An efficient algorithm (called the revised updated geometric build-up algorithm (RUGB)) to build up a protein structure from atomic distance data is presented and provides an effective way of determining a protein structure with sparse exact distance data. In the algorithm, the condition to determine an unpositioned atom iteratively is relaxed (when compared with the UGB algorithm) and data structure techniques are used to make the algorithm more efficient and effective. The algorithm is tested on a set of proteins selected randomly from the Protein Structure Database-PDB. Results We test a set of proteins selected randomly from the Protein Structure Database-PDB. We show that the numerical errors produced by the new RUGB algorithm are smaller when compared with the errors of the UGB algorithm and that the novel RUGB algorithm has a significantly smaller runtime than the UGB algorithm. Conclusions The RUGB algorithm relaxes the condition for updating and incorporates the data structure for accessing neighbours of an atom. The revisions result in an improvement over the UGB algorithm in two important areas: a reduction on the overall runtime and decrease of the numeric error.
dc.title Protein structure determination via an efficient geometric build-up algorithm
dc.type Journal Article
dc.date.updated 2010-05-18T00:06:08Z
dc.description.version Peer Reviewed
dc.language.rfc3066 en
dc.rights.holder et al.; licensee BioMed Central Ltd.

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