ArticleBMC bioinformatics2015
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Protein Loop Modeling via the Discretizable Distance Geometry Problem with Hydrogen-Based NMR Constraints.ACS omega · 2026Article
- Single-cell 3D genome reconstruction in the haploid setting using rigidity theory.Journal of mathematical biology · 2025Article
- Tandem domain structure determination based on a systematic enumeration of conformations.Scientific reports · 2021Article
- Minimal NMR distance information for rigidity of protein graphs.Discrete applied mathematics (Amsterdam, Netherlands : 1988) · 2019Article
- Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.Journal of biomolecular NMR · 2017Article
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Authors and funding
9 authors.
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Abstract
backgroundThe determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.
resultsIn order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.
conclusionsWe described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.
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