alexa Using amino acid typing to improve the accuracy of NMR structure based assignments
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Proteomics & Bioinformatics

Author(s): Halit Erdoan, Mehmet Serkan Apaydin

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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.

This article was published in Health Informatics and Bioinformatics (HIBIT), 2010 5th International Symposium and referenced in Journal of Proteomics & Bioinformatics

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