RefDB: A database of uniformly referenced protein chemical shifts

By Haiyan Zhang, Stephen Neal, David S. Wishart. Journal of Biomolecular NMR, 2003

439 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1785da7b3b3b466ff40da94fd661c3641f93d890

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Citations in the corpus

Residue-by-residue view of in vitro FUS granules that bind the C-terminal domain of RNA polymerase II (2015, neutral): “With a well understood dependence on the backbone dihedral angles that change with secondary structure (Zhang et al., 2003), the deviation of Ca and Cb chemical shifts from random coil values provides a sensitive estimate of the secondary structure propensity at each position.”
ALS mutations disrupt phase separation mediated by -helical structure in the TDP-43 low complexity C-terminal domain (2016, background): “…induced by interaction (Figure 6B, nine residues positions) are upfield (i.e. negative), consistent with greater helical structure for every residue type (Wang and Jardetzky, 2002; Zhang et al., 2003), strongly suggesting increased helical structure upon assembly across the 321 to 340 region.”
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts (2003, methodology): “While clearly defined protocols do exist (Wishart et al., 1995b; Markley et al., 1998), it is estimated that nearly 25% of newly reported protein 13C and 15N shifts are improperly referenced (Zhang et al., 2003).”
Sensitivity of secondary structure propensities to sequence differences between α‐ and γ‐synuclein: Implications for fibrillation (2006, methodology): “We tested this re-referencing procedure using RefDB, a database of uniformly referenced protein chemical shifts (Zhang et al. 2003) in which most of the chemical shifts are expected to be properly referenced.”
Chemical shift-based methods in NMR structure determination (2018, background): “Here, X ε {backbone, sidechain, through-space}, distanceij is the distance between atoms i and j, αij and βij are the parameters derived from known structures with assigned backbone chemical shifts in the database [99].”
SHIFTX2: significantly improved protein chemical shift prediction (2011, methodology): “) we compiled a preliminary collection of * 300 candidate proteins from a number of sources, including RefDB (Zhang et al. 2003), the SPARTA training set 17 and the SHIFTX training set (Neal et al. 2003).”