Developing a Scoring Function for NMR Structure-based Assignments using Machine Learning

  • Mehmet Çağri Çalpur
  • Hakan Erdoğan
  • Bülent Çatay
  • Bruce R. Donald
  • Mehmet Serkan Apaydin
Conference paper
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 62)

Abstract

Determining the assignment of signals received from the ex- periments (peaks) to speci_c nuclei of the target molecule in Nuclear Magnetic Resonance (NMR1) spectroscopy is an important challenge. Nuclear Vector Replacement (NVR) ([2, 3]) is a framework for structure- based assignments which combines multiple types of NMR data such as chemical shifts, residual dipolar couplings, and NOEs. NVR-BIP [1] is a tool which utilizes a scoring function with a binary integer programming (BIP) model to perform the assignments. In this paper, support vector machines (SVM) and boosting are employed to combine the terms in NVR-BIP's scoring function by viewing the assignment as a classi_ca- tion problem. The assignment accuracies obtained using this approach show that boosting improves the assignment accuracy of NVR-BIP on our data set when RDCs are not available and outperforms SVMs. With RDCs, boosting and SVMs o_er mixed results.

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Mehmet Çağri Çalpur
    • 1
  • Hakan Erdoğan
    • 1
  • Bülent Çatay
    • 1
  • Bruce R. Donald
    • 2
  • Mehmet Serkan Apaydin
    • 1
  1. 1.Faculty of Engineering and Natural SciencesSabanci UniversityIstanbulTurkey
  2. 2.Department of Computer Science Duke University Medical Center, Department of BiochemistryDuke UniversityDurhamUSA

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