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Using amino acid typing to improve the accuracy of NMR structure based assignments

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2 Author(s)
Halit Erdo¿an ; Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli Tuzla, 34956, Istanbul, TURKEY ; Mehmet Serkan Apaydin

Nuclear Magnetic Resonance (NMR1) spectroscopy is an important experimental technique that allows one to study protein structure in solution. An important challenge in NMR protein structure determination is the assignment of NMR peaks to corresponding nuclei. In structure-based assignment (SBA), the aim is to perform the assignments with the help of a homologous protein. NVR-BIP is a tool that uses Nuclear Vector Replacement's (NVR) scoring function and binary integer programming to solve SBA problem. In this work, we introduce a method to improve NVR-BIP's assignment accuracy with amino acid typing. We use CRAACK that takes the chemical shifts of C, N and H atoms and returns the possible amino acids along with their confidence scores. We obtain improved assignment accuracies and our results show the effectiveness of integrating amino acid typing with NVR.

Published in:

Health Informatics and Bioinformatics (HIBIT), 2010 5th International Symposium on

Date of Conference:

20-22 April 2010