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Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique to obtain structural information of a protein. In this technique, an essential step is the backbone resonance assignment and Structure Based Assignment (SBA) aims to solve this problem with the help of a template structure. Nuclear Vector Replacement (NVR) is an NMR protein SBA program, that takes as input and chemical shifts and unambiguous NOEs, as well as RDCs, HD-exchange and TOCSY data. NVR does not utilize chemical shifts although this data is widely available for many proteins. In addition, NVR is a proof-of-principle approach and has been run with specific and manually set parameters for some proteins. NA-NVR-ACO [M. Akhmedov, B.Çatay and M.S. Apaydın, (2015) 1550020.] remedies this problem for the NOE data and standardizes NOE usage, while using an ant colony optimization based algorithm. In this paper, we standardize NA-NVR-ACO’s scoring function by using the same parameters for all the proteins and incorporating chemical shifts. We also use a larger protein database and state-of-the-art chemical shift prediction tools, SHIFTX2 [B. Han, Y. Liu, S.W. Ginzinger and D.S. Wishart, (2011) 43–57.] and SPARTA [Y. Shen and A. Bax, (2010) 13–22], to extract the chemical shift statistics. Other practical improvements include automatizing data file preparation and obtaining a degree of reliability for individual peak-amino acid assignments. Our results show that our improvements bring NA-NVR-ACO closer to a practical tool, able to handle a variety of different data types.
ŞeymaÇetnİkaya 1 ; Ekren, Şeyma Nur 1 ; Apaydın, Mehmet Serkan 2
@article{RO_2016__50_2_341_0,
author = {\c{S}eyma\c{C}etn\.Ikaya and Ekren, \c{S}eyma Nur and Apayd{\i}n, Mehmet Serkan},
title = {Progress in {Nuclear} {Vector} {Replacement} for {NMR} {Protein} {Structure-Based} {Assignments}},
journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
pages = {341--349},
publisher = {EDP-Sciences},
volume = {50},
number = {2},
year = {2016},
doi = {10.1051/ro/2015038},
mrnumber = {3479874},
zbl = {1336.90070},
language = {en},
url = {http://geodesic.mathdoc.fr/articles/10.1051/ro/2015038/}
}
TY - JOUR AU - ŞeymaÇetnİkaya AU - Ekren, Şeyma Nur AU - Apaydın, Mehmet Serkan TI - Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments JO - RAIRO - Operations Research - Recherche Opérationnelle PY - 2016 SP - 341 EP - 349 VL - 50 IS - 2 PB - EDP-Sciences UR - http://geodesic.mathdoc.fr/articles/10.1051/ro/2015038/ DO - 10.1051/ro/2015038 LA - en ID - RO_2016__50_2_341_0 ER -
%0 Journal Article %A ŞeymaÇetnİkaya %A Ekren, Şeyma Nur %A Apaydın, Mehmet Serkan %T Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments %J RAIRO - Operations Research - Recherche Opérationnelle %D 2016 %P 341-349 %V 50 %N 2 %I EDP-Sciences %U http://geodesic.mathdoc.fr/articles/10.1051/ro/2015038/ %R 10.1051/ro/2015038 %G en %F RO_2016__50_2_341_0
ŞeymaÇetnİkaya; Ekren, Şeyma Nur; Apaydın, Mehmet Serkan. Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments. RAIRO - Operations Research - Recherche Opérationnelle, Special issue: Research on Optimization and Graph Theory dedicated to COSI 2013 / Special issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine, Tome 50 (2016) no. 2, pp. 341-349. doi: 10.1051/ro/2015038
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