C. L. Tang, E. Alexov, A. M. Pyle, and B. Honig. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of molecular biology, Academic Press, volume 366, issue 5, pages 1475-1496, 2007. C. Tang, E. Alexov, A. Pyle, and B. Honig. Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation. BIOPHYSICAL JOURNAL, volume 82, issue 1, pages 131A-131A, 2002.