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Molecular docking of porphyrins with cationic limbs on intramolecular G-quadruplex
Yoshinobu Ishikawa1, Eiki Higashi, Hiroshi Morioka
1Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 8620973, Japan. ishikawa@gpo.kumamoto-u.ac.jp
Abstract:
We performed molecular docking simulations of porphyrins with cationic limbs on an intramolecular anti-parallel G-quadruplex and molecular dynamics simulations for the model complexes to explore plausible binding regions and modes. With grid-based scoring, GB/SA scoring and MM-PBSA method, two low-energy binding regions, a groove and a loop, for the porphyrins were identified.
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