Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs)

RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

“…Of these best estimates, those clustered into the left-hand side yield an RMSD of 15 Å or better-a value useful in the assignment of ssRNA-protein binding sites [33]. For values of V CONSTANT P 0.75, the RMSD in this preferred solution space (bottom left-hand corner) is typically 610 Å-a finding of significance due to the fact that success in assigning ssRNA binding residues by modern-day machinelearning approaches is consistently P0.85 [1][2][3].…”

“…9 A similar limitation is faced when considering very long nucleotide sequences for which N > 6. All three of these disadvantages can be offset by using the RNA-LIM procedure as the first leg of a structure evaluation pipeline to produce coarsegrained candidate structures that can be subsequently used for more detailed analysis using higher order approaches [1][2][3][12][13][14][15][20][21][22][23][24]33]. Despite the less common occurrence of very long segments of ssRNA being involved in binding [1,31], the ssRNA sequence size limitation (N 6 6) could be potentially offset by (i) consideration of longer sequences as a set of smaller sequence fragments or (ii) reconfiguration of the ssRNA homopolymer statistics in terms of every second ribonucleotide.…”

“…The fundamental importance of RNA-protein interactions in the chemistry of life 1 [1,2] has spurred development of computational tools capable of predicting both the RNA binding propensities and structures of bound protein-RNA complexes [3][4][5][6]. However, traditional approaches for elucidating protein double-stranded DNA/ RNA interactions [7][8][9] tend to be less successful when applied to single-stranded RNA (ssRNA) 2 molecules [3,10].…”