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BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex

Jeongyeon Seo 1 Jae-Kwan Kim 2 Joonghyun Ryu 2 Carlile Lavor 3 Antonio Mucherino 4 Deok-Soo Kim 1, 2
1 Department of Industrial Engineering [Seoul]
2 Voronoi Diagram Research Center
3 IMECC - Instituto de Matemática, Estatística e Computação Científica [Brésil]
4 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : The molecular distance geometry problem (MDGP) is a fundamental problem in determining molecular structures from the NMR data. We present a heuristic algorithm, the BetaMDGP, which outperforms existing algorithms for solving the MDGP. The BetaMDGP algorithm is based on the beta-complex, which is a geometric construct extracted from the quasi-triangulation derived from the Voronoi diagram of atoms. Starting with an initial tetrahedron defined by the centers of four closely located atoms, the BetaMDGP determines a molecular structure by adding one shell of atoms around the currently determined substructure using the beta-complex. The proposed algorithm has been entirely implemented and tested with atomic arrangements stored in an NMR format created from PDB files. Experimental results are also provided to show the powerful capability of the proposed algorithm.
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https://hal.inria.fr/hal-01093066
Contributor : Antonio Mucherino <>
Submitted on : Wednesday, December 10, 2014 - 10:03:10 AM
Last modification on : Friday, March 6, 2020 - 1:19:35 AM

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  • HAL Id : hal-01093066, version 1

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UNIV-RENNES1 | CNRS | INRIA | IRISA | IRISA-D7 | UR1-UFR-ISTIC | UNIV-RENNES | INSTITUT-TELECOM

Citation

Jeongyeon Seo, Jae-Kwan Kim, Joonghyun Ryu, Carlile Lavor, Antonio Mucherino, et al.. BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex. M.L. Gavrilova; C.J.K. Tan. Transactions on Computational Science XXII, Lecture Notes in Computer Science (8360), Springer, pp.130-155, 2014. ⟨hal-01093066⟩

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