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Tuning interval branch-and-prune for protein structure determination. (English) Zbl 1422.92109
Summary: The interval branch and prune \(i\)BP algorithm for obtaining solutions to the interval discretizable molecular distance geometry problem \(i\)DMDGP has proven itself as a powerful method for molecular structure determination. However, substantial obstacles still must be overcome before \(i\)BP may be employed as a tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant of the \(i\)BP algorithm that leverages existing knowledge of protein structures in order to reduce the size of the effective search space by many orders of magnitude. These improvements are included in a newly released implementation of the \(i\)BP software that aims to provide a solid platform for both research and application of the \(i\)DMDGP.

92D20 Protein sequences, DNA sequences
92-08 Computational methods for problems pertaining to biology
Full Text: DOI
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