13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA

被引:2
|
作者
Icazatti, A. A. [1 ]
Martin, O. A. [1 ]
Villegas, M. [1 ]
Szleifer, I [2 ,3 ,4 ]
Vila, J. A. [1 ]
机构
[1] Univ Nacl San Luis, Inst Matemat Aplicada San Luis, CONICET, RA-5700 San Luis, Argentina
[2] Northwestern Univ, Dept Biomed Engn, Evanston, IL 60208 USA
[3] Northwestern Univ, Chem Life Proc Inst, Evanston, IL 60208 USA
[4] Northwestern Univ, Dept Chem, Evanston, IL 60208 USA
关键词
H-1; PREDICTION; DATABASE;
D O I
10.1093/bioinformatics/bty470
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for evaluating the referencing of RNA C-13 CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Results: Based on an existent method we have implemented an open source python module to correct C-13 CS (from here on C-13(exp)) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one.
引用
收藏
页码:4124 / 4126
页数:3
相关论文
共 50 条
  • [41] A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA
    Frank, Aaron T.
    Law, Sean M.
    Brooks, Charles L., III
    JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (42): : 12168 - 12175
  • [42] Chemical Constituents of Lecythis pisonis (Lecythidaceae) - A New Saponin and Complete 1H and 13C Chemical Shift Assignments
    Duarte, Renne C.
    Matos, Carlos R. R.
    Braz-Filho, Raimundo
    Mathias, Leda
    NATURAL PRODUCT COMMUNICATIONS, 2015, 10 (06) : 871 - 874
  • [43] 1H, 15N and 13C chemical shift assignments of the C-terminal domain of TRADD
    Ning Zhang
    Wensu Yuan
    Jing-Song Fan
    Zhi Lin
    Biomolecular NMR Assignments, 2017, 11 : 281 - 284
  • [44] 1H, 15N and 13C chemical shift assignments of the C-terminal domain of TRADD
    Zhang, Ning
    Yuan, Wensu
    Fan, Jing-Song
    Lin, Zhi
    BIOMOLECULAR NMR ASSIGNMENTS, 2017, 11 (02) : 281 - 284
  • [45] 13C-Detection in RNA bases:: Revealing structure-chemical shift relationships
    Fares, Christophe
    Amata, Irene
    Carlomagno, Teresa
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2007, 129 (51) : 15814 - 15823
  • [46] 13C-detection in RNA bases: Revealing structure-chemical shift relationships
    Farès, Christophe
    Amata, Irene
    Carlomagno, Teresa
    Journal of the American Chemical Society, 2007, 129 (51): : 15814 - 15823
  • [47] Prediction of RNA 1H and 13C Chemical Shifts: A Structure Based Approach
    Frank, Aaron T.
    Bae, Sung-Hun
    Stelzer, Andrew C.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2013, 117 (43): : 13497 - 13506
  • [48] A REINVESTIGATION OF THE C-13-NMR CHEMICAL-SHIFT ASSIGNMENTS OF FLUORANTHENE
    JOHNSTON, MD
    MARTIN, GE
    CASTLE, RN
    SPECTROSCOPY LETTERS, 1988, 21 (08) : 853 - 857
  • [49] C-13 CHEMICAL-SHIFT ASSIGNMENTS OF THE NITRATION PRODUCTS OF PYRENE
    KAPLAN, S
    ORGANIC MAGNETIC RESONANCE, 1981, 15 (02): : 197 - 199
  • [50] 13C NMR chemical shift assignments for substituted 2-azabicyclo[3.3.1]nonan-3-ones
    Quirante, J
    Escolano, C
    Diaba, F
    Torra, M
    Bonjoch, J
    MAGNETIC RESONANCE IN CHEMISTRY, 2000, 38 (10) : 891 - 893