BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Book Sections Year : 2014

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

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.
No file

Dates and versions

hal-01093066 , version 1 (10-12-2014)

Identifiers

  • HAL Id : hal-01093066 , version 1

Cite

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⟩
280 View
0 Download

Share

Gmail Facebook Twitter LinkedIn More