Using amino acid typing to improve the accuracy of NMR structure based assignments. Halit Erdogan, undefined & Apaydin, M. S. In Proc. of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT'10), 2010. IEEE Xplore. abstract bibtex Nuclear Magnetic Resonance (NMR) 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.
@inproceedings{hibit10,
author = {Halit Erdogan, and Mehmet Serkan Apaydin},
title = {{Using amino acid typing to improve the accuracy of NMR structure based assignments}},
booktitle = {Proc. of the 5th International Symposium on Health Informatics and Bioinformatics (HIBIT'10)},
year = {2010},
abstract = {{Nuclear Magnetic Resonance (NMR) 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.}},
publisher = {IEEE Xplore},
}
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