Using a distributed SDP approach to solve simulated protein molecular conformation problems

Xingyuan Fang, Kim Chuan Toh

Research output: Chapter in Book/Report/Conference proceedingChapter

6 Citations (Scopus)

Abstract

This chapter presents various enhancements to the DISCO algorithm (originally introduced by Leung and Toh(SIAM J. Sci. Comput. 31:4351-4372, 2009) for anchor-free graph realization in) for applications to conformation of protein molecules in. In our enhanced DISCO algorithm for simulated protein molecular conformation problems, we have incorporated distance information derived from chemistry knowledge such as bond lengths and angles to improve the robustness of the algorithm. We also designed heuristics to detect whether a subgroup is well localized and significantly improved the robustness of the stitching process. Tests are performed on molecules taken from the Protein Data Bank. Given only 20% of the interatomic distances less than 6Åthat are corrupted by high level of noises (to simulate noisy distance restraints generated from nuclear magnetic resonance experiments), our improved algorithm is able to reliably and efficiently reconstruct the conformations of large molecules. For instance, given 20% of interatomic distances which are less than 6Åand are corrupted with 20% multiplicative noise, a 5,600-atom conformation problem is solved in about 30min with a root-mean-square deviation (RMSD) of less than 1Å.

Original languageEnglish (US)
Title of host publicationDistance Geometry
Subtitle of host publicationTheory, Methods, and Applications
PublisherSpringer New York
Pages351-376
Number of pages26
Volume9781461451280
ISBN (Electronic)9781461451280
ISBN (Print)1461451272, 9781461451273
DOIs
StatePublished - Nov 1 2013

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Molecular Conformation
Conformation
Protein
Molecules
Root mean square deviation
Robustness
Stitching
Nuclear Magnetic Resonance
Multiplicative Noise
Chemistry
Enhancement
Subgroup
Heuristics
Angle
Graph in graph theory
Experiment

All Science Journal Classification (ASJC) codes

  • Mathematics(all)

Cite this

Fang, X., & Toh, K. C. (2013). Using a distributed SDP approach to solve simulated protein molecular conformation problems. In Distance Geometry: Theory, Methods, and Applications (Vol. 9781461451280, pp. 351-376). Springer New York. https://doi.org/10.1007/978-1-4614-5128-0_17
Fang, Xingyuan ; Toh, Kim Chuan. / Using a distributed SDP approach to solve simulated protein molecular conformation problems. Distance Geometry: Theory, Methods, and Applications. Vol. 9781461451280 Springer New York, 2013. pp. 351-376
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Fang, X & Toh, KC 2013, Using a distributed SDP approach to solve simulated protein molecular conformation problems. in Distance Geometry: Theory, Methods, and Applications. vol. 9781461451280, Springer New York, pp. 351-376. https://doi.org/10.1007/978-1-4614-5128-0_17

Using a distributed SDP approach to solve simulated protein molecular conformation problems. / Fang, Xingyuan; Toh, Kim Chuan.

Distance Geometry: Theory, Methods, and Applications. Vol. 9781461451280 Springer New York, 2013. p. 351-376.

Research output: Chapter in Book/Report/Conference proceedingChapter

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Fang X, Toh KC. Using a distributed SDP approach to solve simulated protein molecular conformation problems. In Distance Geometry: Theory, Methods, and Applications. Vol. 9781461451280. Springer New York. 2013. p. 351-376 https://doi.org/10.1007/978-1-4614-5128-0_17