A novel knowledge-based potential for RNA 3D structure evaluation

Yang Yi^{1, 2}, Gu Qi², Zhang Ben-Gong³, Shi Ya-Zhou^{2, 3, †}, Shao Zhi-Gang^{1, ‡}

(color online) (a) Energy distribution of distance between N1 of adenine and N3 of uracil. (b) Diagram of representative distance between N1 of adenine and N3 of uracil. (c) Base-stacking and base-pairing energies between each possible base-pair calculated by the proposed potential for 434D. (d) Secondary structure and 3D structure of 434D.