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

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

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

Content Provider	IEEE Xplore Digital Library
Author	Erdogan, H. Apaydin, M.S.
Copyright Year	2010
Description	Author affiliation: Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli Tuzla, 34956, Istanbul, TURKEY (Erdogan, H.; Apaydin, M.S.)
Abstract	Nuclear Magnetic Resonance $(NMR^{1})$ 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 [1] is a tool that uses Nuclear Vector Replacement's (NVR) ([9], [10]) 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.
Starting Page	206
Ending Page	210
File Size	174781
Page Count	5
File Format	PDF
ISBN	9781424459681
e-ISBN	9781424459704
DOI	10.1109/HIBIT.2010.5478879
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-04-20
Publisher Place	Turkey
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Spectroscopy Protein engineering Magnetic resonance Biological systems Amino acids Linear programming Biochemistry Nuclear magnetic resonance Crystallography Chemicals
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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