RNA-LIM is a new procedure for coarse-grained estimation of the structure of single-stranded-RNA (ss-RNA) bound to the surface of a protein. Capable of utilizing any type of pseudo-potential describing the affinity between ss-RNA and surface amino acids, RNA-LIM evolves an ss-RNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. The optimal routes are found by application of a set of minimal ‘limiting’ restraints derived jointly from (1) selective sampling of the ribonucleotide-amino acid affinity pseudo-potential data, and (2) RNA structural specification obtained from a statistical potential gathered from a library of ss-RNA-protein structures. We describe the general approach using a NAST-like approximation of the ss-RNA chain [Jonikas et al. 2009 Bioinformatics 15, 189-199] and a generalized pseudo-potential reflecting the location of a nucleic acid binding site. Minimum and maximum performance indicators of the methodology are established using synthetic data for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded. Some potential uses and extensions of the routine are discussed.
Hall, D., Li, S., Yamashita, K., Azuma, R., Carver, J. A., & Standley, D. M. (2014). A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein. Biophysical chemistry.