cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.
We developed our residue-separation-based CG statistical potentials (cgRNASP) at several CG levels:
(i) three CG beads at P, C4’, and N9 atoms for purine (or N1 atom for pyrimidine);
(ii) two CG beads at P and C4’ atoms;
(iii) one CG bead on C4’ atom.
Correspondingly, for simplicity, our CG statistical potentials were named as cgRNASP, cgRNASP-PC, and cgRNASP-C, respectively. The first potential was named in such way since the potential of 3-bead representation was regarded as a representative one of the CG potentials.
Please follow the readmes in the corresponding subfolders for using the respective statistical potentials. And the potentials were set to a high value of 30 kBT for atom pairs within 3 Å to exclude the structure candidates with severe steric conflicts; updated on August 8, 2024.
Please feel free to contact us if you have any question! zjtan@whu.edu.cn
Reference:
[1] Tan YL, Wang X, Yu S, Zhang B, & Tan ZJ. 2023. cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation. NAR Genom Bioinform. 5(1): lqad016.