Using amino acid typing to improve the accuracy of NMR structure based assignments
Erdoğan, Halit and Apaydın, Serkan Mehmet (2010) Using amino acid typing to improve the accuracy of NMR structure based assignments. In: 5th International Symposium on Health Informatics and Bioinformatics (HIBIT), Antalya, Türkiye
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Official URL: http://dx.doi.org/10.1109/HIBIT.2010.5478879
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.
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