期刊论文

Zhao, YJ;Gong, Z

英文

PHYSICAL CHEMISTRY CHEMICAL PHYSICS

1463-9076

2023

25

41

27967-27980

10.1039/d3cp03384h

This work is supported by the National Natural Science Foundation of China 12175081 (YZ), 31971155 (ZG), Fundamental Research Funds for the Central Universities CCNU22QN004 (YZ), Youth Innovation Promotion Association of the Chinese Academy of Sciences 202 [12175081, 31971155]; National Natural Science Foundation of China [CCNU22QN004]; Fundamental Research Funds for the Central Universities [2020329]; Youth Innovation Promotion Association of the Chinese Academy of Sciences [2022YBZZ043]; Excellent doctorial dissertation cultivation grant from Central China Normal University

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Designing inhibitors for RNA is still challenging due to the bottleneck of maintaining the binding interaction of inhibitor-RNA accompanied by subtle RNA flexibility. Thus, the current approach usually needs to screen thousands of candidate inhibitors for binding. Here, we propose a dynamic geometry design approach to enrich the hits with only a tiny pool of designed geometrically compatible scaffold candidates. First, our method uses graph-based tree decomposition to explore the complementarity rigid binding cyclic peptide and design the amino acid side chain length and charge to fit the RNA ...